Nucleic acid encoding 238p1b2 useful in detecting cancer

ABSTRACT

A novel gene (designated 238P1B2) and its encoded protein, and variants thereof, are described wherein 238P1B2 exhibits tissue specific expression in normal adult tissue, and is aberrantly expressed in the cancers listed in Table I. Consequently, 238P1B2 provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 238P1B2 gene or fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response; antibodies or T cells reactive with 238P1B2 can be used in active or passive immunization.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a division of U.S. patent application Ser. No.12/429,012, filed Apr. 23, 2009, now allowed, which is a continuation ofU.S. patent application Ser. No. 11/483,302, filed Jul. 6, 2006, nowU.S. Pat. No. 7,553,814, issued Jun. 30, 2009, which is a continuationof U.S. patent application Ser. No. 10/114,669, filed Apr. 1, 2002. Thecontents of each application listed in this paragraph are fullyincorporated by reference herein.

REFERENCE TO SEQUENCE LISTING SUBMITTED VIA EFS-WEB

The entire content of the following electronic submission of thesequence listing via the USPTO EFS-WEB server, as authorized and setforth in MPEP §1730 II.B.2(a)(C), is incorporated herein by reference inits entirety for all purposes. The sequence listing is identified on theelectronically filed text file as follows:

Date of File Name Creation Size (bytes) 511582006510Seqlist.txt May 1,2010 1,481,903 bytes

FIELD OF THE INVENTION

The invention described herein relates to a gene and its encodedprotein, termed 238P1B2, expressed in certain cancers, and to diagnosticand therapeutic methods and compositions useful in the management ofcancers that express 238P1B2.

BACKGROUND OF THE INVENTION

Cancer is the second leading cause of human death next to coronarydisease. Worldwide, millions of people die from cancer every year. Inthe United States alone, as reported by the American Cancer Society,cancer causes the death of well over a half-million people annually,with over 1.2 million new cases diagnosed per year. While deaths fromheart disease have been declining significantly, those resulting fromcancer generally are on the rise. In the early part of the next century,cancer is predicted to become the leading cause of death.

Worldwide, several cancers stand out as the leading killers. Inparticular, carcinomas of the lung, prostate, breast, colon, pancreas,and ovary represent the primary causes of cancer death. These andvirtually all other carcinomas share a common lethal feature. With veryfew exceptions, metastatic disease from a carcinoma is fatal. Moreover,even for those cancer patients who initially survive their primarycancers, common experience has shown that their lives are dramaticallyaltered. Many cancer patients experience strong anxieties driven by theawareness of the potential for recurrence or treatment failure. Manycancer patients experience physical debilitations following treatment.Furthermore, many cancer patients experience a recurrence.

Worldwide, prostate cancer is the fourth most prevalent cancer in men.In North America and Northern Europe, it is by far the most commoncancer in males and is the second leading cause of cancer death in men.In the United States alone, well over 30,000 men die annually of thisdisease—second only to lung cancer. Despite the magnitude of thesefigures, there is still no effective treatment for metastatic prostatecancer. Surgical prostatectomy, radiation therapy, hormone ablationtherapy, surgical castration and chemotherapy continue to be the maintreatment modalities. Unfortunately, these treatments are ineffectivefor many and are often associated with undesirable consequences.

On the diagnostic front, the lack of a prostate tumor marker that canaccurately detect early-stage, localized tumors remains a significantlimitation in the diagnosis and management of this disease. Although theserum prostate specific antigen (PSA) assay has been a very useful tool,however its specificity and general utility is widely regarded aslacking in several important respects.

Progress in identifying additional specific markers for prostate cancerhas been improved by the generation of prostate cancer xenografts thatcan recapitulate different stages of the disease in mice. The LAPC (LosAngeles Prostate Cancer) xenografts are prostate cancer xenografts thathave survived passage in severe combined immune deficient (SCID) miceand have exhibited the capacity to mimic the transition from androgendependence to androgen independence (Klein et al., 1997, Nat. Med.3:402). More recently identified prostate cancer markers include PCTA-1(Su et al., 1996, Proc. Natl. Acad. Sci. USA 93: 7252),prostate-specific membrane (PSM) antigen (Pinto et al., Clin Cancer Res1996 September 2 (9): 1445-51), STEAP (Hubert, et al., Proc Natl AcadSci USA. 1999 Dec. 7; 96(25): 14523-8) and prostate stem cell antigen(PSCA) (Reiter et al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).

While previously identified markers such as PSA, PSM, PCTA and PSCA havefacilitated efforts to diagnose and treat prostate cancer, there is needfor the identification of additional markers and therapeutic targets forprostate and related cancers in order to further improve diagnosis andtherapy.

Renal cell carcinoma (RCC) accounts for approximately 3 percent of adultmalignancies. Once adenomas reach a diameter of 2 to 3 cm, malignantpotential exists. In the adult, the two principal malignant renal tumorsare renal cell adenocarcinoma and transitional cell carcinoma of therenal pelvis or ureter. The incidence of renal cell adenocarcinoma isestimated at more than 29,000 cases in the United States, and more than11,600 patients died of this disease in 1998. Transitional cellcarcinoma is less frequent, with an incidence of approximately 500 casesper year in the United States.

Surgery has been the primary therapy for renal cell adenocarcinoma formany decades. Until recently, metastatic disease has been refractory toany systemic therapy. With recent developments in systemic therapies,particularly immunotherapies, metastatic renal cell carcinoma may beapproached aggressively in appropriate patients with a possibility ofdurable responses. Nevertheless, there is a remaining need for effectivetherapies for these patients.

Of all new cases of cancer in the United States, bladder cancerrepresents approximately 5 percent in men (fifth most common neoplasm)and 3 percent in women (eighth most common neoplasm). The incidence isincreasing slowly, concurrent with an increasing older population. In1998, there was an estimated 54,500 cases, including 39,500 in men and15,000 in women. The age-adjusted incidence in the United States is 32per 100,000 for men and 8 per 100,000 in women. The historic male/femaleratio of 3:1 may be decreasing related to smoking patterns in women.There were an estimated 11,000 deaths from bladder cancer in 1998 (7,800in men and 3,900 in women). Bladder cancer incidence and mortalitystrongly increase with age and will be an increasing problem as thepopulation becomes more elderly.

Most bladder cancers recur in the bladder. Bladder cancer is managedwith a combination of transurethral resection of the bladder (TUR) andintravesical chemotherapy or immunotherapy. The multifocal and recurrentnature of bladder cancer points out the limitations of TUR. Mostmuscle-invasive cancers are not cured by TUR alone. Radical cystectomyand urinary diversion is the most effective means to eliminate thecancer but carry an undeniable impact on urinary and sexual function.There continues to be a significant need for treatment modalities thatare beneficial for bladder cancer patients.

An estimated 130,200 cases of colorectal cancer occurred in 2000 in theUnited States, including 93,800 cases of colon cancer and 36,400 ofrectal cancer. Colorectal cancers are the third most common cancers inmen and women. Incidence rates declined significantly during 1992-1996(−2.1% per year). Research suggests that these declines have been due toincreased screening and polyp removal, preventing progression of polypsto invasive cancers. There were an estimated 56,300 deaths (47,700 fromcolon cancer, 8,600 from rectal cancer) in 2000, accounting for about11% of all U.S. cancer deaths.

At present, surgery is the most common form of therapy for colorectalcancer, and for cancers that have not spread, it is frequently curative.Chemotherapy, or chemotherapy plus radiation, is given before or aftersurgery to most patients whose cancer has deeply perforated the bowelwall or has spread to the lymph nodes. A permanent colostomy (creationof an abdominal opening for elimination of body wastes) is occasionallyneeded for colon cancer and is infrequently required for rectal cancer.There continues to be a need for effective diagnostic and treatmentmodalities for colorectal cancer.

There were an estimated 164,100 new cases of lung and bronchial cancerin 2000, accounting for 14% of all U.S. cancer diagnoses. The incidencerate of lung and bronchial cancer is declining significantly in men,from a high of 86.5 per 100,000 in 1984 to 70.0 in 1996. In the 1990s,the rate of increase among women began to slow. In 1996, the incidencerate in women was 42.3 per 100,000.

Lung and bronchial cancer caused an estimated 156,900 deaths in 2000,accounting for 28% of all cancer deaths. During 1992-1996, mortalityfrom lung cancer declined significantly among men (−1.7% per year) whilerates for women were still significantly increasing (0.9% per year).Since 1987, more women have died each year of lung cancer than breastcancer, which, for over 40 years, was the major cause of cancer death inwomen. Decreasing lung cancer incidence and mortality rates most likelyresulted from decreased smoking rates over the previous 30 years;however, decreasing smoking patterns among women lag behind those ofmen. Of concern, although the declines in adult tobacco use have slowed,tobacco use in youth is increasing again.

Treatment options for lung and bronchial cancer are determined by thetype and stage of the cancer and include surgery, radiation therapy, andchemotherapy. For many localized cancers, surgery is usually thetreatment of choice. Because the disease has usually spread by the timeit is discovered, radiation therapy and chemotherapy are often needed incombination with surgery. Chemotherapy alone or combined with radiationis the treatment of choice for small cell lung cancer; on this regimen,a large percentage of patients experience remission, which in some casesis long lasting. There is however, an ongoing need for effectivetreatment and diagnostic approaches for lung and bronchial cancers.

An estimated 182,800 new invasive cases of breast cancer were expectedto occur among women in the United States during 2000. Additionally,about 1,400 new cases of breast cancer were expected to be diagnosed inmen in 2000. After increasing about 4% per year in the 1980s, breastcancer incidence rates in women have leveled off in the 1990s to about110.6 cases per 100,000.

In the U.S. alone, there were an estimated 41,200 deaths (40,800 women,400 men) in 2000 due to breast cancer. Breast cancer ranks second amongcancer deaths in women. According to the most recent data, mortalityrates declined significantly during 1992-1996 with the largest decreasesin younger women, both white and black. These decreases were probablythe result of earlier detection and improved treatment.

Taking into account the medical circumstances and the patient'spreferences, treatment of breast cancer may involve lumpectomy (localremoval of the tumor) and removal of the lymph nodes under the arm;mastectomy (surgical removal of the breast) and removal of the lymphnodes under the arm; radiation therapy; chemotherapy; or hormonetherapy. Often, two or more methods are used in combination. Numerousstudies have shown that, for early stage disease, long-term survivalrates after lumpectomy plus radiotherapy are similar to survival ratesafter modified radical mastectomy. Significant advances inreconstruction techniques provide several options for breastreconstruction after mastectomy. Recently, such reconstruction has beendone at the same time as the mastectomy.

Local excision of ductal carcinoma in situ (DCIS) with adequate amountsof surrounding normal breast tissue may prevent the local recurrence ofthe DCIS. Radiation to the breast and/or tamoxifen may reduce the chanceof DCIS occurring in the remaining breast tissue. This is importantbecause DCIS, if left untreated, may develop into invasive breastcancer. Nevertheless, there are serious side effects or sequelae tothese treatments. There is, therefore, a need for efficacious breastcancer treatments.

There were an estimated 23,100 new cases of ovarian cancer in the UnitedStates in 2000. It accounts for 4% of all cancers among women and rankssecond among gynecologic cancers. During 1992-1996, ovarian cancerincidence rates were significantly declining. Consequent to ovariancancer, there were an estimated 14,000 deaths in 2000. Ovarian cancercauses more deaths than any other cancer of the female reproductivesystem.

Surgery, radiation therapy, and chemotherapy are treatment options forovarian cancer. Surgery usually includes the removal of one or bothovaries, the fallopian tubes (salpingo-oophorectomy), and the uterus(hysterectomy). In some very early tumors, only the involved ovary willbe removed, especially in young women who wish to have children. Inadvanced disease, an attempt is made to remove all intra-abdominaldisease to enhance the effect of chemotherapy. There continues to be animportant need for effective treatment options for ovarian cancer.

There were an estimated 28,300 new cases of pancreatic cancer in theUnited States in 2000. Over the past 20 years, rates of pancreaticcancer have declined in men. Rates among women have remainedapproximately constant but may be beginning to decline. Pancreaticcancer caused an estimated 28,200 deaths in 2000 in the United States.Over the past 20 years, there has been a slight but significant decreasein mortality rates among men (about −0.9% per year) while rates haveincreased slightly among women.

Surgery, radiation therapy, and chemotherapy are treatment options forpancreatic cancer. These treatment options can extend survival and/orrelieve symptoms in many patients but are not likely to produce a curefor most. There is a significant need for additional therapeutic anddiagnostic options for pancreatic cancer.

SUMMARY OF THE INVENTION

The present invention relates to a gene, designated 238P1B2, that hasnow been found to be over-expressed in the cancer(s) listed in Table I.Northern blot expression analysis of 238P1B2 gene expression in normaltissues shows a restricted expression pattern in adult tissues. Thenucleotide (FIG. 2) and amino acid (FIG. 2, and FIG. 3) sequences of238P1B2 are provided. The tissue-related profile of 238P1B2 in normaladult tissues, combined with the over-expression observed in the tumorslisted in Table I, shows that 238P1B2 is aberrantly over-expressed in atleast some cancers, and thus serves as a useful diagnostic,prophylactic, prognostic, and/or therapeutic target for cancers of thetissue(s) such as those listed in Table I.

The invention provides polynucleotides corresponding or complementary toall or part of the 238P1B2 genes, mRNAs, and/or coding sequences,preferably in isolated form, including polynucleotides encoding238P1B2-related proteins and fragments of 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25contiguous amino acids; at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80,85, 90, 95, 100 or more than 100 contiguous amino acids of a238P1B2-related protein, as well as the peptides/proteins themselves;DNA, RNA, DNA/RNA hybrids, and related molecules, polynucleotides oroligonucleotides complementary or having at least a 90% homology to the238P1B2 genes or mRNA sequences or parts thereof, and polynucleotides oroligonucleotides that hybridize to the 238P1B2 genes, mRNAs, or to238P1B2-encoding polynucleotides. Also provided are means for isolatingcDNAs and the genes encoding 238P1B2. Recombinant DNA moleculescontaining 238P1B2 polynucleotides, cells transformed or transduced withsuch molecules, and host-vector systems for the expression of 238P1B2gene products are also provided. The invention further providesantibodies that bind to 238P1B2 proteins and polypeptide fragmentsthereof, including polyclonal and monoclonal antibodies, murine andother mammalian antibodies, chimeric antibodies, humanized and fullyhuman antibodies, and antibodies labeled with a detectable marker ortherapeutic agent. In certain embodiments there is a proviso that theentire nucleic acid sequence of FIG. 2 is not encoded and/or the entireamino acid sequence of FIG. 2 is not prepared. In certain embodiments,the entire nucleic acid sequence of FIG. 2 is encoded and/or the entireamino acid sequence of FIG. 2 is prepared, either of which are inrespective human unit dose forms.

The invention further provides methods for detecting the presence andstatus of 238P1B2 polynucleotides and proteins in various biologicalsamples, as well as methods for identifying cells that express 238P1B2.A typical embodiment of this invention provides methods for monitoring238P1B2 gene products in a tissue or hematology sample having orsuspected of having some form of growth dysregulation such as cancer.

The invention further provides various immunogenic or therapeuticcompositions and strategies for treating cancers that express 238P1B2such as cancers of tissues listed in Table I, including therapies aimedat inhibiting the transcription, translation, processing or function of238P1B2 as well as cancer vaccines. In one aspect, the inventionprovides compositions, and methods comprising them, for treating acancer that expresses 238P1B2 in a human subject wherein the compositioncomprises a carrier suitable for human use and a human unit dose of oneor more than one agent that inhibits the production or function of238P1B2. Preferably, the carrier is a uniquely human carrier. In anotheraspect of the invention, the agent is a moiety that is immunoreactivewith 238P1B2 protein. Non-limiting examples of such moieties include,but are not limited to, antibodies (such as single chain, monoclonal,polyclonal, humanized, chimeric, or human antibodies), functionalequivalents thereof (whether naturally occurring or synthetic), andcombinations thereof. The antibodies can be conjugated to a diagnosticor therapeutic moiety. In another aspect, the agent is a small moleculeas defined herein.

In another aspect, the agent comprises one or more than one peptidewhich comprises a cytotoxic T lymphocyte (CTL) epitope that binds an HLAclass I molecule in a human to elicit a CTL response to 238P1B2 and/orone or more than one peptide which comprises a helper T lymphocyte (HTL)epitope which binds an HLA class II molecule in a human to elicit an HTLresponse. The peptides of the invention may be on the same or on one ormore separate polypeptide molecules. In a further aspect of theinvention, the agent comprises one or more than one nucleic acidmolecule that expresses one or more than one of the CTL or HTL responsestimulating peptides as described above. In yet another aspect of theinvention, the one or more than one nucleic acid molecule may express amoiety that is immunologically reactive with 238P1B2 as described above.The one or more than one nucleic acid molecule may also be, or encodes,a molecule that inhibits production of 238P1B2. Non-limiting examples ofsuch molecules include, but are not limited to, those complementary to anucleotide sequence essential for production of 238P1B2 (e.g. antisensesequences or molecules that form a triple helix with a nucleotide doublehelix essential for 238P1B2 production) or a ribozyme effective to lyse238P1B2 mRNA.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. The 238P1B2 SSH sequence of 210 nucleotides (SEQ ID: 8869).

FIG. 2. The cDNA (SEQ ID: 8870) and amino acid sequence (SEQ ID: 8871)of 238P1B2 variant 1A is shown in FIG. 2A. The start methionine isunderlined. The open reading frame extends from nucleic acids 2133 to2897 including the stop codon. The nucleic acid (SEQ ID: 8872) and aminoacid sequence (SEQ ID: 8873) of 238P1B2 variant 1B is shown in FIG. 2B.The open reading frame extends from nucleic acid 1947 to 2897 includingthe stop codon. The nucleic acid (SEQ ID: 8874) and amino acid (SEQ ID:8875) sequence of 238P1B2 variant 2 is shown in FIG. 2C; the codon forthe start methionine is underlined. The open reading frame extends fromnucleic acid 2133 to 2897 including the stop codon. The nucleic acid(SEQ ID: 8876) and amino acid (SEQ ID: 8877) sequence of 238P1B2 variant3 is shown in FIG. 2D, the codon for the start methionine is underlined.The open reading frame extends from nucleic acid 2133 to 2897 includingthe stop codon. The nucleic acid (SEQ ID: 8878) and amino acid (SEQ ID:8879) sequence of 238P1B2 variant 4 is shown in FIG. 2E; the codon forthe start methionine is underlined. The open reading frame extends fromnucleic acid 2133 to 2897 including the stop codon. The nucleic acid(SEQ ID: 8880) and amino acid (SEQ ID: 8881) sequence of 238P1B2 variant5 is shown in FIG. 2F; the codon for the start methionine is underlined.The open reading frame extends from nucleic acid 2133 to 2897 includingthe stop codon. The nucleic acid (SEQ ID: 8882) and amino acid (SEQ ID:8883) sequence of 238P1B2 variant 6 is shown in FIG. 2G, the codon forthe start methionine is underlined. The open reading frame extends fromnucleic acid 2133 to 2897 including the stop codon.

FIG. 3. Amino acid sequence of 238P1B2 variant 1A (SEQ ID: 8884) isshown in FIG. 3A; it has 254 amino acids. The amino acid sequence of238P1B2 variant 1B (SEQ ID: 8885) is shown in FIG. 3B; it has 316 aminoacids. The amino acid sequence of 238P1B2 variant 2 (SEQ ID: 8886) isshown in FIG. 3C; it has 254 amino acids.

FIG. 4. A. Nucleic Acid sequence alignment of 238P1B2 variant 1 (SEQ ID:8887) with mouse olfactory receptor MOR14-1 (SEQ ID: 8888). B. NucleicAcid sequence alignment of 238P1B2 variant 1 (SEQ ID: 8889) with mouseolfactory receptor MOR14-10 (SEQ ID: 8890). C. Amino Acid sequencealignment of 238P1B2 v.1A (SEQ ID: 8891) with mouse olfactory receptorMOR14-1 (SEQ ID: 8892). D. Amino Acid sequence alignment of 238P1B2 v.1A(SEQ ID: 8893) with prostate specific GPCR PHOR-1 (SEQ ID: 8894). E.Amino acid sequence alignment of 238P1B2 variant 1 (SEQ ID: 8895) withhuman olfactory receptor 5112 (SEQ ID: 8896). F. Amino Acid sequenceClustal Alignment of the three 238P1B2 variants (238P1B2 v.1A (SEQ ID:8897); 238P1B2 v.1B (SEQ ID: 8898); 238P1B2 v.2 (SEQ ID: 8899)),depicting that 238P1B2 V1B contains an additional 62 aa at itsN-terminus relative to V1A, and that 238P1B2 V2 carries a I to T pointmutation at aa 225 relative to V1A

FIG. 5. Hydrophilicity amino acid profile of A) 238P1B2 and B) 238P1B2var1A determined by computer algorithm sequence analysis using themethod of Hopp and Woods (Hopp T. P., Woods K. R., 1981. Proc. Natl.Acad. Sci. U.S.A. 78:3824-3828) accessed on the Protscale website on theworld wide web through the ExPasy molecular biology server.

FIG. 6. Hydropathicity amino acid profile of A) 238P1B2 and B) 238P1B2var1A determined by computer algorithm sequence analysis using themethod of Kyte and Doolittle (Kyte J., Doolittle R. F., 1982. J. Mol.Biol. 157:105-132) accessed on the ProtScale website on the world wideweb through the ExPasy molecular biology server.

FIG. 7. Percent accessible residues amino acid profile of A) 238P1B2 andB) 238P1B2 var1A determined by computer algorithm sequence analysisusing the method of Janin (Janin J., 1979 Nature 277:491-492) accessedon the ProtScale website on the world wide web through the ExPasymolecular biology server.

FIG. 8. Average flexibility amino acid profile of A) 238P1B2 and B)238P1B2 var1A determined by computer algorithm sequence analysis usingthe method of Bhaskaran and Ponnuswamy (Bhaskaran R., and Ponnuswamy P.K., 1988. Int. J. Pept. Protein Res. 32:242-255) accessed on theProtScale website on the world wide web(.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biologyserver.

FIG. 9. Beta-turn amino acid profile of A) 238P1B2 and B) 238P1B2 var1Adetermined by computer algorithm sequence analysis using the method ofDeleage and Roux (Deleage, G., Roux B. 1987 Protein Engineering1:289-294) accessed on the ProtScale website through the ExPasymolecular biology server.

FIG. 10. Schematic display of nucleotide variants of 238P1B2. Variant238P1B2 v.2 through 238P1B2 v.6 are variants with single nucleotidevariations. Black box shows the same sequence as 238P1B2 v.1. Numberscorrespond to those of 238P1B2 v.1. SNPs are indicated above the box.

FIG. 11. Schematic display of protein variants of 238P1B2. Nucleotidevariant 238P1B2 v.1 in FIG. 10 codes for protein variants 238P1B2 v.1Aand v.1B. Nucleotide variant 238P1B2 v.2 in FIG. 10 codes for proteinvariant 238P1B2 v.2. Black box shows the same sequence as 238P1B2 v.1.Numbers in “( )” underneath the box correspond to those of 238P1B2 v.1A.Single amino acid differences are indicated above the box.

FIG. 12. A, B. Secondary structure prediction for 238P1B2 variant 1a(SEQ ID: 8901) and variant 1b (SEQ ID: 8902). The secondary structuresof 238P1B2 variant 1a (A) and of variant 1b (B) proteins were predictedusing the HNN—Hierarchical Neural Network method (Guermeur, 1997),accessed from the ExPasy molecular biology server. This method predictsthe presence and location of alpha helices, extended strands, and randomcoils from the primary protein sequence. The percent of the protein in agiven secondary structure is also listed for each variant.

C, D, E, F. Transmembrane prediction for 238P1B2 variant 1a and 1b. C,E. Schematic representations of the probability of existence oftransmembrane regions and orientation of 238P1B2 variant 1a (C) andvariant 1b (E) based on the TMpred algorithm of Hofmann and Stoffelwhich utilizes TMBASE (K. Hofmann, W. Stoffel. TMBASE—A database ofmembrane spanning protein segments Biol. Chem. Hoppe-Seyler 374:166,1993). D, F. Schematic representation of the probability of theexistence of transmembrane regions and the extracellular andintracellular orientation of 238P1B2 variant 1a (D) and variant 1b (F)based on the TMHMM algorithm of Sonnhammer, von Heijne, and Krogh (ErikL. L. Sonnhammer, Gunnar von Heijne, and Anders Krogh: A hidden Markovmodel for predicting transmembrane helices in protein sequences. InProc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology,p 175-182 Ed J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D.Sankoff, and C. Sensen Menlo Park, Calif.: AAAI Press, 1998). The TMpredand TMHMM algorithms are accessed from the ExPasy molecular biologyserver. The results of the transmembrane prediction programs presenteddepict 238P1B2 variant 1a as most likely containing 6 transmembranedomains and variant 1b 7 transmembrane domains.

FIG. 13: Probable topology and structure of 238P1B2 variants 1 and 1B.

FIG. 14. Expression of 238P1B2 by RT-PCR. First strand cDNA was preparedfrom vital pool 1 (liver, lung and kidney), vital pool 2 (pancreas,colon and stomach), and prostate cancer pool. Normalization wasperformed by PCR using primers to actin and GAPDH. Semi-quantitativePCR, using primers to 238P1B2, was performed at 26 and 30 cycles ofamplification. Results show strong expression of 238P1B2 in prostatecancer pool but not in vital pool 1 and vital pool 2.

FIG. 15. Expression of 238P1B2 in normal tissues. Two multiple tissuenorthern blots (Clontech) both with 2 μg of mRNA/lane were probed withthe 238P1B2 SSH fragment. Size standards in kilobases (kb) are indicatedon the side. Results show absence of 238P1B2 expression in all 16 normaltissues tested.

FIG. 16. Expression of 238P1B2 in Multiple Normal Tissues. An mRNA dotblot containing 76 different samples from human tissues was analyzedusing a 238P1B2 SSH probe. Expression was only detected in placenta.

FIG. 17. Expression of 238P1B2 in Human Patient Cancer Specimens andNormal Tissues. RNA was extracted from a pool of three prostate cancerpatient specimens, as well as from normal prostate (NP), normal bladder(NB), normal kidney (NK), normal colon (NC), normal lung (NL), normalbreast (NBr), and normal ovary (NO. Northern blot with 10 μg of totalRNA/lane was probed with 238P1B2 SSH sequence. Size standards inkilobases (kb) are indicated on the side. The results show expression of238P1B2 in the prostate cancer pool and normal ovary.

FIG. 18. Expression of 238P1B2 in prostate cancer patient tissues. RNAwas extracted from normal prostate (N), prostate cancer xenografts(LAPC-4AD, LAPC-4AI, LAPC-9AD, LAPC-9AI), prostate cancer cell lines(LNCaP and PC3), and prostate cancer patient tumors (T). Northern blotswith 10 μg of total RNA were probed with the 238P1B2 SSH fragment. Sizestandards in kilobases are on the side. Results show strong expressionof 238P1B2 in prostate tumor tissues. The lower panel represents theethidium bromide staining of the gel.

DETAILED DESCRIPTION OF THE INVENTION

Outline of Sections

I.) Definitions

II.) 238P1B2 Polynucleotides

-   -   II.A.) Uses of 238P1B2 Polynucleotides        -   II.A.1.) Monitoring of Genetic Abnormalities        -   II.A.2.) Antisense Embodiments        -   II.A.3.) Primers and Primer Pairs        -   II.A.4.) Isolation of 238P1B2-Encoding Nucleic Acid            Molecules        -   II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector            Systems

III.) 238P1B2-related Proteins

-   -   III.A.) Motif-bearing Protein Embodiments    -   III.B.) Expression of 238P1B2-related Proteins    -   III.C.) Modifications of 238P1B2-related Proteins    -   III.D.) Uses of 238P1B2-related Proteins

IV.) 238P1B2 Antibodies

V.) 238P1B2 Cellular Immune Responses

VI.) 238P1B2 Transgenic Animals

VII.) Methods for the Detection of 238P1B2

VIII.) Methods for Monitoring the Status of 238P1B2-related Genes andTheir Products

IX.) Identification of Molecules That Interact With 238P1B2

X.) Therapeutic Methods and Compositions

-   -   X.A.) Anti-Cancer Vaccines    -   X.B.) 238P1B2 as a Target for Antibody-Based Therapy    -   X.C.) 238P1B2 as a Target for Cellular Immune Responses        -   X.C.1. Minigene Vaccines        -   X.C.2. Combinations of CTL Peptides with Helper Peptides        -   X.C.3. Combinations of CTL Peptides with T Cell Priming            Agents        -   X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL            and/or HTL Peptides    -   X.D.) Adoptive Immunotherapy    -   X.E.) Administration of Vaccines for Therapeutic or Prophylactic        Purposes

XI.) Diagnostic and Prognostic Embodiments of 238P1B2.

XII.) Inhibition of 238P1B2 Protein Function

-   -   XII.A.) Inhibition of 238P1B2 With Intracellular Antibodies    -   XII.B.) Inhibition of 238P1B2 with Recombinant Proteins    -   XII.C.) Inhibition of 238P1B2 Transcription or Translation    -   XII.D.) General Considerations for Therapeutic Strategies

XIII.) KITS

I.) Definitions

Unless otherwise defined, all terms of art, notations and otherscientific terms or terminology used herein are intended to have themeanings commonly understood by those of skill in the art to which thisinvention pertains. In some cases, terms with commonly understoodmeanings are defined herein for clarity and/or for ready reference, andthe inclusion of such definitions herein should not necessarily beconstrued to represent a substantial difference over what is generallyunderstood in the art. Many of the techniques and procedures describedor referenced herein are well understood and commonly employed usingconventional methodology by those skilled in the art, such as, forexample, the widely utilized molecular cloning methodologies describedin Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd. edition(1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. Asappropriate, procedures involving the use of commercially available kitsand reagents are generally carried out in accordance with manufacturerdefined protocols and/or parameters unless otherwise noted.

The terms “advanced prostate cancer”, “locally advanced prostatecancer”, “advanced disease” and “locally advanced disease” mean prostatecancers that have extended through the prostate capsule, and are meantto include stage C disease under the American Urological Association(AUA) system, stage C1-C2 disease under the Whitmore-Jewett system, andstage T3-T4 and N+ disease under the TNM (tumor, node, metastasis)system. In general, surgery is not recommended for patients with locallyadvanced disease, and these patients have substantially less favorableoutcomes compared to patients having clinically localized(organ-confined) prostate cancer. Locally advanced disease is clinicallyidentified by palpable evidence of induration beyond the lateral borderof the prostate, or asymmetry or induration above the prostate base.Locally advanced prostate cancer is presently diagnosed pathologicallyfollowing radical prostatectomy if the tumor invades or penetrates theprostatic capsule, extends into the surgical margin, or invades theseminal vesicles.

“Altering the native glycosylation pattern” is intended for purposesherein to mean deleting one or more carbohydrate moieties found innative sequence 238P1B2 (either by removing the underlying glycosylationsite or by deleting the glycosylation by chemical and/or enzymaticmeans), and/or adding one or more glycosylation sites that are notpresent in the native sequence 238P1B2. In addition, the phrase includesqualitative changes in the glycosylation of the native proteins,involving a change in the nature and proportions of the variouscarbohydrate moieties present.

The term “analog” refers to a molecule which is structurally similar orshares similar or corresponding attributes with another molecule (e.g. a238P1B2-related protein). For example an analog of a 238P1B2 protein canbe specifically bound by an antibody or T cell that specifically bindsto 238P1B2.

The term “antibody” is used in the broadest sense. Therefore an“antibody” can be naturally occurring or man-made such as monoclonalantibodies produced by conventional hybridoma technology. Anti-238P1B2antibodies comprise monoclonal and polyclonal antibodies as well asfragments containing the antigen-binding domain and/or one or morecomplementarity determining regions of these antibodies.

An “antibody fragment” is defined as at least a portion of the variableregion of the immunoglobulin molecule that binds to its target, i.e.,the antigen-binding region. In one embodiment it specifically coverssingle anti-238P1B2 antibodies and clones thereof (including agonist,antagonist and neutralizing antibodies) and anti-238P1B2 antibodycompositions with polyepitopic specificity.

The term “codon optimized sequences” refers to nucleotide sequences thathave been optimized for a particular host species by replacing anycodons having a usage frequency of less than about 20%. Nucleotidesequences that have been optimized for expression in a given hostspecies by elimination of spurious polyadenylation sequences,elimination of exon/intron splicing signals, elimination oftransposon-like repeats and/or optimization of GC content in addition tocodon optimization are referred to herein as an “expression enhancedsequences.”

The term “cytotoxic agent” refers to a substance that inhibits orprevents the expression activity of cells, function of cells and/orcauses destruction of cells. The term is intended to include radioactiveisotopes chemotherapeutic agents, and toxins such as small moleculetoxins or enzymatically active toxins of bacterial, fungal, plant oranimal origin, including fragments and/or variants thereof. Examples ofcytotoxic agents include, but are not limited to maytansinoids, yttrium,bismuth, ricin, ricin A-chain, doxorubicin, daunorubicin, taxol,ethidium bromide, mitomycin, etoposide, tenoposide, vincristine,vinblastine, colchicine, dihydroxy anthracin dione, actinomycin,diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin Achain, modeccin A chain, alpha-sarcin, gelonin, mitogellin,retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin,sapaonaria officinalis inhibitor, and glucocorticoid and otherchemotherapeutic agents, as well as radioisotopes such as At²¹¹, I¹³¹,I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³² and radioactive isotopes ofLu. Antibodies may also be conjugated to an anti-cancer pro-drugactivating enzyme capable of converting the pro-drug to its active form.

The term “homolog” refers to a molecule which exhibits homology toanother molecule, by for example, having sequences of chemical residuesthat are the same or similar at corresponding positions.

“Human Leukocyte Antigen” or “HLA” is a human class I or class II MajorHistocompatibility Complex (MHC) protein (see, e.g., Stites, et al.,IMMUNOLOGY, 8^(TH) ED., Lange Publishing, Los Altos, Calif. (1994).

The terms “hybridize”, “hybridizing”, “hybridizes” and the like, used inthe context of polynucleotides, are meant to refer to conventionalhybridization conditions, preferably such as hybridization in 50%formamide/6×SSC/0.1% SDS/100 μg/ml ssDNA, in which temperatures forhybridization are above 37 degrees C. and temperatures for washing in0.1×SSC/0.1% SDS are above 55 degrees C.

The phrases “isolated” or “biologically pure” refer to material which issubstantially or essentially free from components which normallyaccompany the material as it is found in its native state. Thus,isolated peptides in accordance with the invention preferably do notcontain materials normally associated with the peptides in their in situenvironment. For example, a polynucleotide is said to be “isolated” whenit is substantially separated from contaminant polynucleotides thatcorrespond or are complementary to genes other than the 238P1B2 genes orthat encode polypeptides other than 238P1B2 gene product or fragmentsthereof. A skilled artisan can readily employ nucleic acid isolationprocedures to obtain an isolated 238P1B2 polynucleotide. A protein issaid to be “isolated,” for example, when physical, mechanical orchemical methods are employed to remove the 238P1B2 proteins fromcellular constituents that are normally associated with the protein. Askilled artisan can readily employ standard purification methods toobtain an isolated 238P1B2 protein. Alternatively, an isolated proteincan be prepared by chemical means.

The term “mammal” refers to any organism classified as a mammal,including mice, rats, rabbits, dogs, cats, cows, horses and humans. Inone embodiment of the invention, the mammal is a mouse. In anotherembodiment of the invention, the mammal is a human.

The terms “metastatic prostate cancer” and “metastatic disease” meanprostate cancers that have spread to regional lymph nodes or to distantsites, and are meant to include stage D disease under the AUA system andstage T×N×M+ under the TNM system. As is the case with locally advancedprostate cancer, surgery is generally not indicated for patients withmetastatic disease, and hormonal (androgen ablation) therapy is apreferred treatment modality. Patients with metastatic prostate cancereventually develop an androgen-refractory state within 12 to 18 monthsof treatment initiation. Approximately half of these androgen-refractorypatients die within 6 months after developing that status. The mostcommon site for prostate cancer metastasis is bone. Prostate cancer bonemetastases are often osteoblastic rather than osteolytic (i.e.,resulting in net bone formation). Bone metastases are found mostfrequently in the spine, followed by the femur, pelvis, rib cage, skulland humerus. Other common sites for metastasis include lymph nodes,lung, liver and brain. Metastatic prostate cancer is typically diagnosedby open or laparoscopic pelvic lymphadenectomy, whole body radionuclidescans, skeletal radiography, and/or bone lesion biopsy.

The term “monoclonal antibody” refers to an antibody obtained from apopulation of substantially homogeneous antibodies, i.e., the antibodiescomprising the population are identical except for possible naturallyoccurring mutations that are present in minor amounts.

A “motif”, as in biological motif of an 238P1B2-related protein, refersto any pattern of amino acids forming part of the primary sequence of aprotein, that is associated with a particular function (e.g.protein-protein interaction, protein-DNA interaction, etc) ormodification (e.g. that is phosphorylated, glycosylated or amidated), orlocalization (e.g. secretory sequence, nuclear localization sequence,etc.) or a sequence that is correlated with being immunogenic, eitherhumorally or cellularly. A motif can be either contiguous or capable ofbeing aligned to certain positions that are generally correlated with acertain function or property. In the context of HLA motifs, “motif”refers to the pattern of residues in a peptide of defined length,usually a peptide of from about 8 to about 13 amino acids for a class IHLA motif and from about 6 to about 25 amino acids for a class II HLAmotif, which is recognized by a particular HLA molecule. Peptide motifsfor HLA binding are typically different for each protein encoded by eachhuman HLA allele and differ in the pattern of the primary and secondaryanchor residues.

A “pharmaceutical excipient” comprises a material such as an adjuvant, acarrier, pH-adjusting and buffering agents, tonicity adjusting agents,wetting agents, preservative, and the like.

“Pharmaceutically acceptable” refers to a non-toxic, inert, and/orcomposition that is physiologically compatible with humans or othermammals.

The term “polynucleotide” means a polymeric form of nucleotides of atleast 10 bases or base pairs in length, either ribonucleotides ordeoxynucleotides or a modified form of either type of nucleotide, and ismeant to include single and double stranded forms of DNA and/or RNA. Inthe art, this term if often used interchangeably with “oligonucleotide”.A polynucleotide can comprise a nucleotide sequence disclosed hereinwherein thymine (T), as shown for example in FIG. 2, can also be uracil(U); this definition pertains to the differences between the chemicalstructures of DNA and RNA, in particular the observation that one of thefour major bases in RNA is uracil (U) instead of thymine (T).

The term “polypeptide” means a polymer of at least about 4, 5, 6, 7, or8 amino acids. Throughout the specification, standard three letter orsingle letter designations for amino acids are used. In the art, thisterm is often used interchangeably with “peptide” or “protein”.

An HLA “primary anchor residue” is an amino acid at a specific positionalong a peptide sequence which is understood to provide a contact pointbetween the immunogenic peptide and the HLA molecule. One to three,usually two, primary anchor residues within a peptide of defined lengthgenerally defines a “motif” for an immunogenic peptide. These residuesare understood to fit in close contact with peptide binding groove of anHLA molecule, with their side chains buried in specific pockets of thebinding groove. In one embodiment, for example, the primary anchorresidues for an HLA class I molecule are located at position 2 (from theamino terminal position) and at the carboxyl terminal position of a 8,9, 10, 11, or 12 residue peptide epitope in accordance with theinvention. In another embodiment, for example, the primary anchorresidues of a peptide that will bind an HLA class II molecule are spacedrelative to each other, rather than to the termini of a peptide, wherethe peptide is generally of at least 9 amino acids in length. Theprimary anchor positions for each motif and supermotif are set forth inTable IV. For example, analog peptides can be created by altering thepresence or absence of particular residues in the primary and/orsecondary anchor positions shown in Table IV. Such analogs are used tomodulate the binding affinity and/or population coverage of a peptidecomprising a particular HLA motif or supermotif.

A “recombinant” DNA or RNA molecule is a DNA or RNA molecule that hasbeen subjected to molecular manipulation in vitro.

Non-limiting examples of small molecules include compounds that bind orinteract with 238P1B2, ligands including hormones, neuropeptides,chemokines, odorants, phospholipids, and functional equivalents thereofthat bind and preferably inhibit 238P1B2 protein function. Suchnon-limiting small molecules preferably have a molecular weight of lessthan about 10 kDa, more preferably below about 9, about 8, about 7,about 6, about 5 or about 4 kDa. In certain embodiments, small moleculesphysically associate with, or bind, 238P1B2 protein; are not found innaturally occurring metabolic pathways; and/or are more soluble inaqueous than non-aqueous solutions

“Stringency” of hybridization reactions is readily determinable by oneof ordinary skill in the art, and generally is an empirical calculationdependent upon probe length, washing temperature, and saltconcentration. In general, longer probes require higher temperatures forproper annealing, while shorter probes need lower temperatures.Hybridization generally depends on the ability of denatured nucleic acidsequences to reanneal when complementary strands are present in anenvironment below their melting temperature. The higher the degree ofdesired homology between the probe and hybridizable sequence, the higherthe relative temperature that can be used. As a result, it follows thathigher relative temperatures would tend to make the reaction conditionsmore stringent, while lower temperatures less so. For additional detailsand explanation of stringency of hybridization reactions, see Ausubel etal., Current Protocols in Molecular Biology, Wiley IntersciencePublishers, (1995).

“Stringent conditions” or “high stringency conditions”, as definedherein, are identified by, but not limited to, those that: (1) employlow ionic strength and high temperature for washing, for example 0.015 Msodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at50° C.; (2) employ during hybridization a denaturing agent, such asformamide, for example, 50% (v/v) formamide with 0.1% bovine serumalbumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphatebuffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodiumcitrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate,5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS,and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC(sodium chloride/sodium. citrate) and 50% formamide at 55° C., followedby a high-stringency wash consisting of 0.1×SSC containing EDTA at 55°C. “Moderately stringent conditions” are described by, but not limitedto, those in Sambrook et al., Molecular Cloning: A Laboratory Manual,New York: Cold Spring Harbor Press, 1989, and include the use of washingsolution and hybridization conditions (e.g., temperature, ionic strengthand % SDS) less stringent than those described above. An example ofmoderately stringent conditions is overnight incubation at 37° C. in asolution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodiumcitrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10%dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA,followed by washing the filters in 1×SSC at about 37-50° C. The skilledartisan will recognize how to adjust the temperature, ionic strength,etc. as necessary to accommodate factors such as probe length and thelike.

An HLA “supermotif” is a peptide binding specificity shared by HLAmolecules encoded by two or more HLA alleles.

As used herein “to treat” or “therapeutic” and grammatically relatedterms, refer to any improvement of any consequence of disease, such asprolonged survival, less morbidity, and/or a lessening of side effectswhich are the byproducts of an alternative therapeutic modality; fulleradication of disease is not required.

A “transgenic animal” (e.g., a mouse or rat) is an animal having cellsthat contain a transgene, which transgene was introduced into the animalor an ancestor of the animal at a prenatal, e.g., an embryonic stage. A“transgene” is a DNA that is integrated into the genome of a cell fromwhich a transgenic animal develops.

As used herein, an HLA or cellular immune response “vaccine” is acomposition that contains or encodes one or more peptides of theinvention. There are numerous embodiments of such vaccines, such as acocktail of one or more individual peptides; one or more peptides of theinvention comprised by a polyepitopic peptide; or nucleic acids thatencode such individual peptides or polypeptides, e.g., a minigene thatencodes a polyepitopic peptide. The “one or more peptides” can includeany whole unit integer from 1-150 or more, e.g., at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100,105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 or more peptides ofthe invention. The peptides or polypeptides can optionally be modified,such as by lipidation, addition of targeting or other sequences. HLAclass I peptides of the invention can be admixed with, or linked to, HLAclass II peptides, to facilitate activation of both cytotoxic Tlymphocytes and helper T lymphocytes. HLA vaccines can also comprisepeptide-pulsed antigen presenting cells, e.g., dendritic cells.

The term “variant” refers to a molecule that exhibits a variation from adescribed type or norm, such as a protein that has one or more differentamino acid residues in the corresponding position(s) of a specificallydescribed protein (e.g. the 238P1B2 protein shown in FIG. 2 or FIG. 3.An analog is an example of a variant protein. Splice isoforms and singlenucleotides polymorphisms (SNPs) are further examples of variants.

The “238P1B2-related proteins” of the invention include thosespecifically identified herein, as well as allelic variants,conservative substitution variants, analogs and homologs that can beisolated/generated and characterized without undue experimentationfollowing the methods outlined herein or readily available in the art.Fusion proteins that combine parts of different 238P1B2 proteins orfragments thereof, as well as fusion proteins of a 238P1B2 protein and aheterologous polypeptide are also included. Such 238P1B2 proteins arecollectively referred to as the 238P1B2-related proteins, the proteinsof the invention, or 238P1B2. The term “238P1B2-related protein” refersto a polypeptide fragment or an 238P1B2 protein sequence of 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, ormore than 25 amino acids; or, at least 30, 35, 40, 45, 50, 55, 60, 65,70, 80, 85, 90, 95, 100 or more than 100 amino acids.

II.) 238P1B2 Polynucleotides

One aspect of the invention provides polynucleotides corresponding orcomplementary to all or part of an 238P1B2 gene, mRNA, and/or codingsequence, preferably in isolated form, including polynucleotidesencoding an 238P1B2-related protein and fragments thereof, DNA, RNA,DNA/RNA hybrid, and related molecules, polynucleotides oroligonucleotides complementary to an 238P1B2 gene or mRNA sequence or apart thereof, and polynucleotides or oligonucleotides that hybridize toan 238P1B2 gene, mRNA, or to an 238P1B2 encoding polynucleotide(collectively, “238P1B2 polynucleotides”). In all instances whenreferred to in this section, T can also be U in FIG. 2.

Embodiments of a 238P1B2 polynucleotide include: a 238P1B2polynucleotide having the sequence shown in FIG. 2, the nucleotidesequence of 238P1B2 as shown in FIG. 2 wherein T is U; at least 10contiguous nucleotides of a polynucleotide having the sequence as shownin FIG. 2; or, at least 10 contiguous nucleotides of a polynucleotidehaving the sequence as shown in FIG. 2 where T is U. For example,embodiments of 238P1B2 nucleotides comprise, without limitation:

(I) a polynucleotide comprising, consisting essentially of, orconsisting of a sequence as shown in FIG. 2, wherein T can also be U;

-   -   (II) a polynucleotide comprising, consisting essentially of, or        consisting of the sequence as shown in FIG. 2A, from nucleotide        residue number 2133 through nucleotide residue number 2894,        followed by a stop codon, wherein T can also be U;    -   (III) a polynucleotide comprising, consisting essentially of, or        consisting of the sequence as shown in FIG. 2B, from nucleotide        residue number 1947 through nucleotide residue number 2894,        followed by a stop codon, wherein T can also be U;    -   (IV) a polynucleotide comprising, consisting essentially of, or        consisting of the sequence as shown in FIG. 2C, from nucleotide        residue number 2133 through nucleotide residue number 2894,        followed by a stop codon, wherein T can also be U;    -   (V) a polynucleotide comprising, consisting essentially of, or        consisting of the sequence as shown in FIG. 2D, from nucleotide        residue number 2133 through nucleotide residue number 2894,        followed by a stop codon, wherein T can also be U;    -   (VI) a polynucleotide comprising, consisting essentially of, or        consisting of the sequence as shown in FIG. 2E, from nucleotide        residue number 2133 through nucleotide residue number 2894,        followed by a stop codon, wherein T can also be U;    -   (VII) a polynucleotide comprising, consisting essentially of, or        consisting of the sequence as shown in FIG. 2F, from nucleotide        residue number 2133 through nucleotide residue number 2894,        followed by a stop codon, wherein T can also be U;    -   (VIII) a polynucleotide comprising, consisting essentially of,        or consisting of the sequence as shown in FIG. 2G, from        nucleotide residue number 2133 through nucleotide residue number        2894, followed by a stop codon, wherein T can also be U;    -   (IX) a polynucleotide that encodes an 238P1B2-related protein        that is at least 90% homologous to an entire amino acid sequence        shown in FIG. 2A-G;    -   (X) a polynucleotide that encodes an 238P1B2-related protein        that is at least 90% identical to an entire amino acid sequence        shown in FIG. 2A-G;    -   (XI) a polynucleotide that encodes at least one peptide set        forth in Tables V-XVIII or Table XIX;    -   (XII) a polynucleotide that encodes a peptide region of at least        5 amino acids of a peptide of FIG. 3A in any whole number        increment up to 254 that includes an amino acid position having        a value greater than 0.5 in the Hydrophilicity profile of FIG.        5A, or of FIG. 3B in any whole number increment up to 316 that        includes an amino acid position having a value greater than 0.5        in the Hydrophilicity profile of FIG. 5B;    -   (XIII) a polynucleotide that encodes a peptide region of at        least 5 amino acids of a peptide of FIG. 3A in any whole number        increment up to 254 that includes an amino acid position having        a value less than 0.5 in the Hydropathicity profile of FIG. 6A,        or of FIG. 3B in any whole number increment up to 316, that        includes an amino acid position having a value less than 0.5 in        the Hydropathicity profile of FIG. 6B;    -   (XIV) a polynucleotide that encodes a peptide region of at least        5 amino acids of a peptide of FIG. 3A in any whole number        increment up to 254 that includes an amino acid position having        a value greater than 0.5 in the Percent Accessible Residues        profile of FIG. 7A, or of FIG. 3B in any whole number increment        up to 316, that includes an amino acid position having a value        greater than 0.5 in the Percent Accessible Residues profile of        FIG. 7B;    -   (XV) a polynucleotide that encodes a peptide region of at least        5 amino acids of a peptide of FIG. 3A in any whole number        increment up to 254 that includes an amino acid position having        a value greater than 0.5 in the Average Flexibility profile on        FIG. 8A, or of FIG. 3B in any whole number increment up to 316,        that includes an amino acid position having a value greater than        0.5 in the Average Flexibility profile on FIG. 8B;    -   (XVI) a polynucleotide that encodes a peptide region of at least        5 amino acids of a peptide of FIG. 3A in any whole number        increment up to 254 that includes an amino acid position having        a value greater than 0.5 in the Beta-turn profile of FIG. 9A, or        of FIG. 3B in any whole number increment up to 316, that        includes an amino acid position having a value greater than 0.5        in the Beta-turn profile of FIG. 9B;    -   (XVII) a polynucleotide that encodes a 238P1B2-related protein        whose sequence is encoded by the cDNAs contained in the plasmid        deposited with American Type Culture Collection as Accession No.        PTA-4124 on Mar. 7, 2002;    -   (XVIII) a polynucleotide that is fully complementary to a        polynucleotide of any one of (I)-(XVII);    -   (XIX) a polynucleotide that selectively hybridizes under        stringent conditions to a polynucleotide of (I)-(XVIII);    -   (XX) a peptide that is encoded by any of (I)-(XIX); and,    -   (XXI) a polynucleotide of any of (I)-(XIX) or peptide of (XX)        together with a pharmaceutical excipient and/or in a human unit        dose form.

As used herein, a range is understood to specifically disclose all wholeunit positions thereof.

Typical embodiments of the invention disclosed herein include 238P1B2polynucleotides that encode specific portions of 238P1B2 mRNA sequences(and those which are complementary to such sequences) such as those thatencode the proteins and/or fragments thereof, for example:

-   -   (a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,        20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,        80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140,        145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205,        210, 215, 220, 225, 230, 235, 240, 245, 250, or 254 contiguous        amino acids of 238P1B2;    -   (b) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,        20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,        80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140,        145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205,        210, 215, 220, 225, 230, 235, 240, 245, 250, or 254 contiguous        amino acids of variant IA;    -   (c) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,        20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,        80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140,        145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205,        210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270,        275, 280, 285, 290, 295, 300, 305, 310, 315, or 316 contiguous        amino acids of variant 1B; or    -   (d) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,        20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,        80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140,        145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205,        210, 215, 220, 225, 230, 235, 240, 245, 250, or 254 contiguous        amino acids of variant 2.

For example, representative embodiments of the invention disclosedherein include: polynucleotides and their encoded peptides themselvesencoding about amino acid 1 to about amino acid 10 of the 238P1B2protein or variants shown in FIG. 2 or FIG. 3, polynucleotides encodingabout amino acid 10 to about amino acid 20 of the 238P1B2 protein orvariants shown in FIG. 2 or FIG. 3, polynucleotides encoding about aminoacid 20 to about amino acid 30 of the 238P1B2 protein or variants shownin FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 30 toabout amino acid 40 of the 238P1B2 protein or variants shown in FIG. 2or FIG. 3, polynucleotides encoding about amino acid 40 to about aminoacid 50 of the 238P1B2 protein or variants shown in FIG. 2 or FIG. 3,polynucleotides encoding about amino acid 50 to about amino acid 60 ofthe 238P1B2 protein or variants shown in FIG. 2 or FIG. 3,polynucleotides encoding about amino acid 60 to about amino acid 70 ofthe 238P1B2 protein or variants shown in FIG. 2 or FIG. 3,polynucleotides encoding about amino acid 70 to about amino acid 80 ofthe 238P1B2 protein or variants shown in FIG. 2 or FIG. 3,polynucleotides encoding about amino acid 80 to about amino acid 90 ofthe 238P1B2 protein or variants shown in FIG. 2 or FIG. 3,polynucleotides encoding about amino acid 90 to about amino acid 100 ofthe 238P1B2 protein or variants shown in FIG. 2 or FIG. 3, or encodingregions from about amino acid 100 to amino acids later in the sequence,in increments of about 10 amino acids, ending at the carboxyl terminalamino acid set forth in FIG. 2 or FIG. 3. Accordingly polynucleotidesencoding portions of the amino acid sequence (of about 10 amino acids),of amino acids 100 through the carboxyl terminal amino acid of the238P1B2 protein are embodiments of the invention. Wherein it isunderstood that each particular amino acid position discloses thatposition plus or minus five amino acid residues.

Polynucleotides encoding relatively long portions of a 238P1B2 proteinare also within the scope of the invention. For example, polynucleotidesencoding from about amino acid 1 (or 20 or 30 or 40 etc.) to about aminoacid 20, (or 30, or 40 or 50 etc.) of the 238P1B2 protein or variantsshown in FIG. 2 or FIG. 3 can be generated by a variety of techniqueswell known in the art. These polynucleotide fragments can include anyportion of the 238P1B2 sequence or variants as shown in FIG. 2.

Additional illustrative embodiments of the invention disclosed hereininclude 238P1B2 polynucleotide fragments encoding one or more of thebiological motifs contained within a 238P1B2 protein sequence or variantsequence, including one or more of the motif-bearing subsequences of a238P1B2 protein or variant set forth in Tables V-XVIII and Table XIX.

Note that to determine the starting position of any peptide set forth inTables V-XVIII and Table XIX (collectively HLA Peptide Tables)respective to its parental protein, e.g., variant 1, variant 2, etc.,reference is made to three factors: the particular variant, the lengthof the peptide in an HLA Peptide Table, and the Search Peptides listedat the beginning of Table XIX. Generally, a unique Search Peptide isused to obtain HLA peptides for a particular variant. The position ofeach Search Peptide relative to its respective parent molecule is listedat the beginning of Table XIX. Accordingly if a Search Peptide begins atposition “X”, one must add the value “X−1” to each position in TablesV-XVIII and Table XIX to obtain the actual position of the HLA peptidesin their parental molecule. For example if a particular Search Peptidebegins at position 150 of its parental molecule, one must add 150−1,i.e., 149 to each HLA peptide amino acid position to calculate theposition of that amino acid in the parent molecule.

One embodiment of the invention comprises an HLA peptide, that occurs atleast twice in Tables V-XVIII and Table XIX collectively, or anoligonucleotide that encodes the HLA peptide. Another embodiment of theinvention comprises an HLA peptide that occurs at least once in TablesV-XVIII and at least once in Table XIX, or an oligonucleotide thatencodes the HLA peptide.

Another embodiment of the invention is antibody epitopes which comprisea peptide region, or an oligonucleotide encoding the peptide region,that has one two, three, four, or five of the following characteristics:

-   -   i) a peptide region of at least 5 amino acids of a particular        peptide of FIG. 3, in any whole number increment up to the full        length of that protein in FIG. 3, that includes an amino acid        position having a value equal to or greater than 0.5, 0.6, 0.7,        0.8, 0.9, or having a value equal to 1.0, in the Hydrophilicity        profile of FIG. 5;    -   ii) a peptide region of at least 5 amino acids of a particular        peptide of FIG. 3, in any whole number increment up to the full        length of that protein in FIG. 3, that includes an amino acid        position having a value equal to or less than 0.5, 0.4, 0.3,        0.2, 0.1, or having a value equal to 0.0, in the Hydropathicity        profile of FIG. 6;    -   iii) a peptide region of at least 5 amino acids of a particular        peptide of FIG. 3, in any whole number increment up to the full        length of that protein in FIG. 3, that includes an amino acid        position having a value equal to or greater than 0.5, 0.6, 0.7,        0.8, 0.9, or having a value equal to 1.0, in the Percent        Accessible Residues profile of FIG. 7;    -   iv) a peptide region of at least 5 amino acids of a particular        peptide of FIG. 3, in any whole number increment up to the full        length of that protein in FIG. 3, that includes an amino acid        position having a value equal to or greater than 0.5, 0.6, 0.7,        0.8, 0.9, or having a value equal to 1.0, in the Average        Flexibility profile of FIG. 8; or    -   v) a peptide region of at least 5 amino acids of a particular        peptide of FIG. 3, in any whole number increment up to the full        length of that protein in FIG. 3, that includes an amino acid        position having a value equal to or greater than 0.5, 0.6, 0.7,        0.8, 0.9, or having a value equal to 1.0, in the Beta-turn        profile of FIG. 9.

In another embodiment, typical polynucleotide fragments of the inventionencode one or more of the regions of 238P1B2 protein or variant thatexhibit homology to a known molecule. In another embodiment of theinvention, typical polynucleotide fragments can encode one or more ofthe 238P1B2 protein or variant N-glycosylation sites, cAMP andcGMP-dependent protein kinase phosphorylation sites, casein kinase IIphosphorylation sites or N-myristoylation site and amidation sites.

II.A.) Uses of 238P1B2 Polynucleotides

II.A.1.) Monitoring of Genetic Abnormalities

The polynucleotides of the preceding paragraphs have a number ofdifferent specific uses. The human 238P1B2 gene maps to the chromosomallocation set forth in Example 3. For example, because the 238P1B2 genemaps to this chromosome, polynucleotides that encode different regionsof the 238P1B2 proteins are used to characterize cytogeneticabnormalities of this chromosomal locale, such as abnormalities that areidentified as being associated with various cancers. In certain genes, avariety of chromosomal abnormalities including rearrangements have beenidentified as frequent cytogenetic abnormalities in a number ofdifferent cancers (see e.g. Krajinovic et al., Mutat. Res. 382(3-4):81-83 (1998); Johansson et al., Blood 86(10): 3905-3914 (1995) andFinger et al., P.N.A.S. 85(23): 9158-9162 (1988)). Thus, polynucleotidesencoding specific regions of the 238P1B2 proteins provide new tools thatcan be used to delineate, with greater precision than previouslypossible, cytogenetic abnormalities in the chromosomal region thatencodes 238P1B2 that may contribute to the malignant phenotype. In thiscontext, these polynucleotides satisfy a need in the art for expandingthe sensitivity of chromosomal screening in order to identify moresubtle and less common chromosomal abnormalities (see e.g. Evans et al.,Am. J. Obstet. Gynecol 171(4): 1055-1057 (1994)).

Furthermore, as 238P1B2 was shown to be highly expressed in bladder andother cancers, 238P1B2 polynucleotides are used in methods assessing thestatus of 238P1B2 gene products in normal versus cancerous tissues.Typically, polynucleotides that encode specific regions of the 238P1B2proteins are used to assess the presence of perturbations (such asdeletions, insertions, point mutations, or alterations resulting in aloss of an antigen etc.) in specific regions of the 238P1B2 gene, suchas regions containing one or more motifs. Exemplary assays include bothRT-PCR assays as well as single-strand conformation polymorphism (SSCP)analysis (see, e.g., Marrogi et al., J. Cutan. Pathol. 26(8): 369-378(1999), both of which utilize polynucleotides encoding specific regionsof a protein to examine these regions within the protein.

II.A.2.) Antisense Embodiments

Other specifically contemplated nucleic acid related embodiments of theinvention disclosed herein are genomic DNA, cDNAs, ribozymes, andantisense molecules, as well as nucleic acid molecules based on analternative backbone, or including alternative bases, whether derivedfrom natural sources or synthesized, and include molecules capable ofinhibiting the RNA or protein expression of 238P1B2. For example,antisense molecules can be RNAs or other molecules, including peptidenucleic acids (PNAs) or non-nucleic acid molecules such asphosphorothioate derivatives, that specifically bind DNA or RNA in abase pair-dependent manner. A skilled artisan can readily obtain theseclasses of nucleic acid molecules using the 238P1B2 polynucleotides andpolynucleotide sequences disclosed herein.

Antisense technology entails the administration of exogenousoligonucleotides that bind to a target polynucleotide located within thecells. The term “antisense” refers to the fact that sucholigonucleotides are complementary to their intracellular targets, e.g.,238P1B2. See for example, Jack Cohen, Oligodeoxynucleotides, AntisenseInhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1:1-5(1988). The 238P1B2 antisense oligonucleotides of the present inventioninclude derivatives such as S-oligonucleotides (phosphorothioatederivatives or S-oligos, see, Jack Cohen, supra), which exhibit enhancedcancer cell growth inhibitory action. S-oligos (nucleosidephosphorothioates) are isoelectronic analogs of an oligonucleotide(O-oligo) in which a nonbridging oxygen atom of the phosphate group isreplaced by a sulfur atom. The S-oligos of the present invention can beprepared by treatment of the corresponding O-oligos with3H-1,2-benzodithiol-3-one-1,1-dioxide, which is a sulfur transferreagent. See, e.g., Iyer, R. P. et al., J. Org. Chem. 55:4693-4698(1990); and Iyer, R. P. et al., J. Am. Chem. Soc. 112:1253-1254 (1990).Additional 238P1B2 antisense oligonucleotides of the present inventioninclude morpholino antisense oligonucleotides known in the art (see,e.g., Partridge et al., 1996, Antisense & Nucleic Acid Drug Development6: 169-175).

The 238P1B2 antisense oligonucleotides of the present inventiontypically can be RNA or DNA that is complementary to and stablyhybridizes with the first 100 5′ codons or last 100 3′ codons of a238P1B2 genomic sequence or the corresponding mRNA. Absolutecomplementarity is not required, although high degrees ofcomplementarity are preferred. Use of an oligonucleotide complementaryto this region allows for the selective hybridization to 238P1B2 mRNAand not to mRNA specifying other regulatory subunits of protein kinase.In one embodiment, 238P1B2 antisense oligonucleotides of the presentinvention are 15 to 30-mer fragments of the antisense DNA molecule thathave a sequence that hybridizes to 238P1B2 mRNA. Optionally, 238P1B2antisense oligonucleotide is a 30-mer oligonucleotide that iscomplementary to a region in the first 10 5′ codons or last 10 3′ codonsof 238P1B2. Alternatively, the antisense molecules are modified toemploy ribozymes in the inhibition of 238P1B2 expression, see, e.g., L.A. Couture & D. T. Stinchcomb; Trends Genet. 12: 510-515 (1996).

II.A.3.) Primers and Primer Pairs

Further specific embodiments of this nucleotides of the inventioninclude primers and primer pairs, which allow the specific amplificationof polynucleotides of the invention or of any specific parts thereof,and probes that selectively or specifically hybridize to nucleic acidmolecules of the invention or to any part thereof. Probes can be labeledwith a detectable marker, such as, for example, a radioisotope,fluorescent compound, bioluminescent compound, a chemiluminescentcompound, metal chelator or enzyme. Such probes and primers are used todetect the presence of a 238P1B2 polynucleotide in a sample and as ameans for detecting a cell expressing a 238P1B2 protein.

Examples of such probes include polypeptides comprising all or part ofthe human 238P1B2 cDNA sequence shown in FIG. 2. Examples of primerpairs capable of specifically amplifying 238P1B2 mRNAs are alsodescribed in the Examples. As will be understood by the skilled artisan,a great many different primers and probes can be prepared based on thesequences provided herein and used effectively to amplify and/or detecta 238P1B2 mRNA.

The 238P1B2 polynucleotides of the invention are useful for a variety ofpurposes, including but not limited to their use as probes and primersfor the amplification and/or detection of the 238P1B2 gene(s), mRNA(s),or fragments thereof; as reagents for the diagnosis and/or prognosis ofprostate cancer and other cancers; as coding sequences capable ofdirecting the expression of 238P1B2 polypeptides; as tools formodulating or inhibiting the expression of the 238P1B2 gene(s) and/ortranslation of the 238P1B2 transcript(s); and as therapeutic agents.

The present invention includes the use of any probe as described hereinto identify and isolate a 238P1B2 or 238P1B2 related nucleic acidsequence from a naturally occurring source, such as humans or othermammals, as well as the isolated nucleic acid sequence per se, whichwould comprise all or most of the sequences found in the probe used.

II.A.4.) Isolation of 238P1B2-Encoding Nucleic Acid Molecules

The 238P1B2 cDNA sequences described herein enable the isolation ofother polynucleotides encoding 238P1B2 gene product(s), as well as theisolation of polynucleotides encoding 238P1B2 gene product homologs,alternatively spliced isoforms, allelic variants, and mutant forms of a238P1B2 gene product as well as polynucleotides that encode analogs of238P1B2-related proteins. Various molecular cloning methods that can beemployed to isolate full length cDNAs encoding an 238P1B2 gene are wellknown (see, for example, Sambrook, J. et al., Molecular Cloning: ALaboratory Manual, 2d edition, Cold Spring Harbor Press, New York, 1989;Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley andSons, 1995). For example, lambda phage cloning methodologies can beconveniently employed, using commercially available cloning systems(e.g., Lambda ZAP Express, Stratagene). Phage clones containing 238P1B2gene cDNAs can be identified by probing with a labeled 238P1B2 cDNA or afragment thereof. For example, in one embodiment, a 238P1B2 cDNA (e.g.,FIG. 2) or a portion thereof can be synthesized and used as a probe toretrieve overlapping and full-length cDNAs corresponding to a 238P1B2gene. A 238P1B2 gene itself can be isolated by screening genomic DNAlibraries, bacterial artificial chromosome libraries (BACs), yeastartificial chromosome libraries (YACs), and the like, with 238P1B2 DNAprobes or primers.

II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems

The invention also provides recombinant DNA or RNA molecules containingan 238P1B2 polynucleotide, a fragment, analog or homologue thereof,including but not limited to phages, plasmids, phagemids, cosmids, YACs,BACs, as well as various viral and non-viral vectors well known in theart, and cells transformed or transfected with such recombinant DNA orRNA molecules. Methods for generating such molecules are well known(see, for example, Sambrook et al., 1989, supra).

The invention further provides a host-vector system comprising arecombinant DNA molecule containing a 238P1B2 polynucleotide, fragment,analog or homologue thereof within a suitable prokaryotic or eukaryotichost cell. Examples of suitable eukaryotic host cells include a yeastcell, a plant cell, or an animal cell, such as a mammalian cell or aninsect cell (e.g., a baculovirus-infectible cell such as an Sf9 orHighFive cell). Examples of suitable mammalian cells include variousprostate cancer cell lines such as DU145 and TsuPr1, other transfectableor transducible prostate cancer cell lines, primary cells (PrEC), aswell as a number of mammalian cells routinely used for the expression ofrecombinant proteins (e.g., COS, CHO, 293, 293T cells). Moreparticularly, a polynucleotide comprising the coding sequence of 238P1B2or a fragment, analog or homolog thereof can be used to generate 238P1B2proteins or fragments thereof using any number of host-vector systemsroutinely used and widely known in the art.

A wide range of host-vector systems suitable for the expression of238P1B2 proteins or fragments thereof are available, see for example,Sambrook et al., 1989, supra; Current Protocols in Molecular Biology,1995, supra). Preferred vectors for mammalian expression include but arenot limited to pcDNA 3.1 myc-His-tag (Invitrogen) and the retroviralvector pSRαtkneo (Muller et al., 1991, MCB 11:1785). Using theseexpression vectors, 238P1B2 can be expressed in several prostate cancerand non-prostate cell lines, including for example 293, 293T, rat-1, NIH3T3 and TsuPr1. The host-vector systems of the invention are useful forthe production of a 238P1B2 protein or fragment thereof. Suchhost-vector systems can be employed to study the functional propertiesof 238P1B2 and 238P1B2 mutations or analogs.

Recombinant human 238P1B2 protein or an analog or homolog or fragmentthereof can be produced by mammalian cells transfected with a constructencoding a 238P1B2-related nucleotide. For example, 293T cells can betransfected with an expression plasmid encoding 238P1B2 or fragment,analog or homolog thereof, a 238P1B2-related protein is expressed in the293T cells, and the recombinant 238P1B2 protein is isolated usingstandard purification methods (e.g., affinity purification usinganti-238P1B2 antibodies). In another embodiment, a 238P1B2 codingsequence is subcloned into the retroviral vector pSRαMSVtkneo and usedto infect various mammalian cell lines, such as NIH 3T3, TsuPr1, 293 andrat-1 in order to establish 238P1B2 expressing cell lines. Various otherexpression systems well known in the art can also be employed.Expression constructs encoding a leader peptide joined in frame to a238P1B2 coding sequence can be used for the generation of a secretedform of recombinant 238P1B2 protein.

As discussed herein, redundancy in the genetic code permits variation in238P1B2 gene sequences. In particular, it is known in the art thatspecific host species often have specific codon preferences, and thusone can adapt the disclosed sequence as preferred for a desired host.For example, preferred analog codon sequences typically have rare codons(i.e., codons having a usage frequency of less than about 20% in knownsequences of the desired host) replaced with higher frequency codons.Codon preferences for a specific species are calculated, for example, byutilizing codon usage tables available on the INTERNET.

Additional sequence modifications are known to enhance proteinexpression in a cellular host. These include elimination of sequencesencoding spurious polyadenylation signals, exon/intron splice sitesignals, transposon-like repeats, and/or other such well-characterizedsequences that are deleterious to gene expression. The GC content of thesequence is adjusted to levels average for a given cellular host, ascalculated by reference to known genes expressed in the host cell. Wherepossible, the sequence is modified to avoid predicted hairpin secondarymRNA structures. Other useful modifications include the addition of atranslational initiation consensus sequence at the start of the openreading frame, as described in Kozak, Mol. Cell. Biol., 9:5073-5080(1989). Skilled artisans understand that the general rule thateukaryotic ribosomes initiate translation exclusively at the 5′ proximalAUG codon is abrogated only under rare conditions (see, e.g., Kozak PNAS92(7): 2662-2666, (1995) and Kozak NAR 15(20): 8125-8148 (1987)).

III.) 238P1B2-Related Proteins

Another aspect of the present invention provides 238P1B2-relatedproteins. Specific embodiments of 238P1B2 proteins comprise apolypeptide having all or part of the amino acid sequence of human238P1B2 as shown in FIG. 2 or FIG. 3. Alternatively, embodiments of238P1B2 proteins comprise variant, homolog or analog polypeptides thathave alterations in the amino acid sequence of 238P1B2 shown in FIG. 2or FIG. 3.

In general, naturally occurring allelic variants of human 238P1B2 sharea high degree of structural identity and homology (e.g., 90% or morehomology). Typically, allelic variants of a 238P1B2 protein containconservative amino acid substitutions within the 238P1B2 sequencesdescribed herein or contain a substitution of an amino acid from acorresponding position in a homologue of 238P1B2. One class of 238P1B2allelic variants are proteins that share a high degree of homology withat least a small region of a particular 238P1B2 amino acid sequence, butfurther contain a radical departure from the sequence, such as anon-conservative substitution, truncation, insertion or frame shift. Incomparisons of protein sequences, the terms, similarity, identity, andhomology each have a distinct meaning as appreciated in the field ofgenetics. Moreover, orthology and paralogy can be important conceptsdescribing the relationship of members of a given protein family in oneorganism to the members of the same family in other organisms.

Amino acid abbreviations are provided in Table II. Conservative aminoacid substitutions can frequently be made in a protein without alteringeither the conformation or the function of the protein. Proteins of theinvention can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15conservative substitutions. Such changes include substituting any ofisoleucine (I), valine (V), and leucine (L) for any other of thesehydrophobic amino acids; aspartic acid (D) for glutamic acid (E) andvice versa; glutamine (Q) for asparagine (N) and vice versa; and serine(S) for threonine (T) and vice versa. Other substitutions can also beconsidered conservative, depending on the environment of the particularamino acid and its role in the three-dimensional structure of theprotein. For example, glycine (G) and alanine (A) can frequently beinterchangeable, as can alanine (A) and valine (V). Methionine (M),which is relatively hydrophobic, can frequently be interchanged withleucine and isoleucine, and sometimes with valine. Lysine (K) andarginine (R) are frequently interchangeable in locations in which thesignificant feature of the amino acid residue is its charge and thediffering pK's of these two amino acid residues are not significant.Still other changes can be considered “conservative” in particularenvironments (see, e.g. Table III herein; pages 13-15 “Biochemistry”2^(nd) ED. Lubert Stryer ed (Stanford University); Henikoff et al., PNAS1992 Vol 89 10915-10919; Lei et al., J Biol Chem 1995 May 19;270(20):11882-6).

Embodiments of the invention disclosed herein include a wide variety ofart-accepted variants or analogs of 238P1B2 proteins such aspolypeptides having amino acid insertions, deletions and substitutions.238P1B2 variants can be made using methods known in the art such assite-directed mutagenesis, alanine scanning, and PCR mutagenesis.Site-directed mutagenesis (Carter et al., Nucl. Acids Res., 13:4331(1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)), cassettemutagenesis (Wells et al., Gene, 34:315 (1985)), restriction selectionmutagenesis (Wells et al., Philos. Trans. R. Soc. London SerA, 317:415(1986)) or other known techniques can be performed on the cloned DNA toproduce the 238P1B2 variant DNA.

Scanning amino acid analysis can also be employed to identify one ormore amino acids along a contiguous sequence that is involved in aspecific biological activity such as a protein-protein interaction.Among the preferred scanning amino acids are relatively small, neutralamino acids. Such amino acids include alanine, glycine, serine, andcysteine. Alanine is typically a preferred scanning amino acid amongthis group because it eliminates the side-chain beyond the beta-carbonand is less likely to alter the main-chain conformation of the variant.Alanine is also typically preferred because it is the most common aminoacid. Further, it is frequently found in both buried and exposedpositions (Creighton, The Proteins, (W.H. Freeman & Co., N.Y.); Chothia,J. Mol. Biol., 150:1 (1976)). If alanine substitution does not yieldadequate amounts of variant, an isosteric amino acid can be used.

As defined herein, 238P1B2 variants, analogs or homologs, have thedistinguishing attribute of having at least one epitope that is “crossreactive” with a 238P1B2 protein having an amino acid sequence of FIG.3. As used in this sentence, “cross reactive” means that an antibody orT cell that specifically binds to an 238P1B2 variant also specificallybinds to a 238P1B2 protein having an amino acid sequence set forth inFIG. 3. A polypeptide ceases to be a variant of a protein shown in FIG.3, when it no longer contains any epitope capable of being recognized byan antibody or T cell that specifically binds to the starting 238P1B2protein. Those skilled in the art understand that antibodies thatrecognize proteins bind to epitopes of varying size, and a grouping ofthe order of about four or five amino acids, contiguous or not, isregarded as a typical number of amino acids in a minimal epitope. See,e.g., Nair et al., J. Immunol. 2000 165(12): 6949-6955; Hebbes et al.,Mol Immunol (1989) 26(9):865-73; Schwartz et al., J Immunol (1985)135(4):2598-608.

Other classes of 238P1B2-related protein variants share 70%, 75%, 80%,85% or 90% or more similarity with an amino acid sequence of FIG. 3, ora fragment thereof. Another specific class of 238P1B2 protein variantsor analogs comprise one or more of the 238P1B2 biological motifsdescribed herein or presently known in the art. Thus, encompassed by thepresent invention are analogs of 238P1B2 fragments (nucleic or aminoacid) that have altered functional (e.g. immunogenic) propertiesrelative to the starting fragment. It is to be appreciated that motifsnow or which become part of the art are to be applied to the nucleic oramino acid sequences of FIG. 2 or FIG. 3.

As discussed herein, embodiments of the claimed invention includepolypeptides containing less than the full amino acid sequence of a238P1B2 protein shown in FIG. 2 or FIG. 3. For example, representativeembodiments of the invention comprise peptides/proteins having any 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids of a238P1B2 protein shown in FIG. 2 or FIG. 3.

Moreover, representative embodiments of the invention disclosed hereininclude polypeptides consisting of about amino acid 1 to about aminoacid 10 of a 238P1B2 protein shown in FIG. 2 or FIG. 3, polypeptidesconsisting of about amino acid 10 to about amino acid 20 of a 238P1B2protein shown in FIG. 2 or FIG. 3, polypeptides consisting of aboutamino acid 20 to about amino acid 30 of a 238P1B2 protein shown in FIG.2 or FIG. 3, polypeptides consisting of about amino acid 30 to aboutamino acid 40 of a 238P1B2 protein shown in FIG. 2 or FIG. 3,polypeptides consisting of about amino acid 40 to about amino acid 50 ofa 238P1B2 protein shown in FIG. 2 or FIG. 3, polypeptides consisting ofabout amino acid 50 to about amino acid 60 of a 238P1B2 protein shown inFIG. 2 or FIG. 3, polypeptides consisting of about amino acid 60 toabout amino acid 70 of a 238P1B2 protein shown in FIG. 2 or FIG. 3,polypeptides consisting of about amino acid 70 to about amino acid 80 ofa 238P1B2 protein shown in FIG. 2 or FIG. 3, polypeptides consisting ofabout amino acid 80 to about amino acid 90 of a 238P1B2 protein shown inFIG. 2 or FIG. 3, polypeptides consisting of about amino acid 90 toabout amino acid 100 of a 238P1B2 protein shown in FIG. 2 or FIG. 3,etc. throughout the entirety of a 238P1B2 amino acid sequence. Moreover,polypeptides consisting of about amino acid 1 (or 20 or 30 or 40 etc.)to about amino acid 20, (or 130, or 140 or 150 etc.) of a 238P1B2protein shown in FIG. 2 or FIG. 3 are embodiments of the invention. Itis to be appreciated that the starting and stopping positions in thisparagraph refer to the specified position as well as that position plusor minus 5 residues.

238P1B2-related proteins are generated using standard peptide synthesistechnology or using chemical cleavage methods well known in the art.Alternatively, recombinant methods can be used to generate nucleic acidmolecules that encode a 238P1B2-related protein. In one embodiment,nucleic acid molecules provide a means to generate defined fragments ofa 238P1B2 protein (or variants, homologs or analogs thereof).

III.A.) Motif-Bearing Protein Embodiments

Additional illustrative embodiments of the invention disclosed hereininclude 238P1B2 polypeptides comprising the amino acid residues of oneor more of the biological motifs contained within a 238P1B2 polypeptidesequence set forth in FIG. 2 or FIG. 3. Various motifs are known in theart, and a protein can be evaluated for the presence of such motifs by anumber of publicly available Internet sites (see, e.g., Epimatrix™ andEpimer™, Brown University, and BIMAS).

Motif bearing subsequences of all 238P1B2 variant proteins are set forthand identified in Tables V-XVIII and Table XIX.

Table XX sets forth several frequently occurring motifs based on pfamsearches (see URL address pfam.wustl.edu/). The columns of Table XX list(1) motif name abbreviation, (2) percent identity found amongst thedifferent member of the motif family, (3) motif name or description and(4) most common function; location information is included if the motifis relevant for location.

Polypeptides comprising one or more of the 238P1B2 motifs discussedabove are useful in elucidating the specific characteristics of amalignant phenotype in view of the observation that the 238P1B2 motifsdiscussed above are associated with growth dysregulation and because238P1B2 is overexpressed in certain cancers (See, e.g., Table I). Caseinkinase II, cAMP and camp-dependent protein kinase, and Protein Kinase C,for example, are enzymes known to be associated with the development ofthe malignant phenotype (see e.g. Chen et al., Lab Invest., 78(2):165-174 (1998); Gaiddon et al., Endocrinology 136(10): 4331-4338 (1995);Hall et al., Nucleic Acids Research 24(6): 1119-1126 (1996); Peterzielet al., Oncogene 18(46): 6322-6329 (1999) and O'Brian, Oncol. Rep. 5(2):305-309 (1998)). Moreover, both glycosylation and myristoylation areprotein modifications also associated with cancer and cancer progression(see e.g. Dennis et al., Biochem. Biophys. Acta 1473(1):21-34 (1999);Raju et al., Exp. Cell Res. 235(1): 145-154 (1997)). Amidation isanother protein modification also associated with cancer and cancerprogression (see e.g. Treston et al., J. Natl. Cancer Inst. Monogr.(13): 169-175 (1992)).

In another embodiment, proteins of the invention comprise one or more ofthe immunoreactive epitopes identified in accordance with art-acceptedmethods, such as the peptides set forth in Tables V-XVIII and Table XIX.CTL epitopes can be determined using specific algorithms to identifypeptides within an 238P1B2 protein that are capable of optimally bindingto specified HLA alleles (e.g., Table IV; Epimatrix™ and Epimer™, BrownUniversity, and BIMAS). Moreover, processes for identifying peptidesthat have sufficient binding affinity for HLA molecules and which arecorrelated with being immunogenic epitopes, are well known in the art,and are carried out without undue experimentation. In addition,processes for identifying peptides that are immunogenic epitopes, arewell known in the art, and are carried out without undue experimentationeither in vitro or in vivo.

Also known in the art are principles for creating analogs of suchepitopes in order to modulate immunogenicity. For example, one beginswith an epitope that bears a CTL or HTL motif (see, e.g., the HLA ClassI and HLA Class II motifs/supermotifs of Table IV). The epitope isanaloged by substituting out an amino acid at one of the specifiedpositions, and replacing it with another amino acid specified for thatposition. For example, one can substitute out a deleterious residue infavor of any other residue, such as a preferred residue as defined inTable IV; substitute a less-preferred residue with a preferred residueas defined in Table IV; or substitute an originally-occurring preferredresidue with another preferred residue as defined in Table IV.Substitutions can occur at primary anchor positions or at otherpositions in a peptide; see, e.g., Table IV.

A variety of references reflect the art regarding the identification andgeneration of epitopes in a protein of interest as well as analogsthereof. See, for example, WO 9733602 to Chesnut et al.; Sette,Immunogenetics 1999 50(3-4): 201-212; Sette et al., J. Immunol. 2001166(2): 1389-1397; Sidney et al., Hum. Immunol. 1997 58(1): 12-20; Kondoet al., Immunogenetics 1997 45(4): 249-258; Sidney et al., J. Immunol.1996 157(8): 3480-90; and Falk et al., Nature 351: 290-6 (1991); Hunt etal., Science 255:1261-3 (1992); Parker et al., J. Immunol. 149:3580-7(1992); Parker et al., J. Immunol. 152:163-75 (1994)); Kast et al., 1994152(8): 3904-12; Borras-Cuesta et al., Hum. Immunol. 2000 61(3):266-278; Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633;Alexander et al., PMID: 7895164, UI: 95202582; O'Sullivan et al., J.Immunol. 1991 147(8): 2663-2669; Alexander et al., Immunity 1994 1(9):751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92.

Related embodiments of the invention include polypeptides comprisingcombinations of the different motifs set forth in Table XXI, and/or, oneor more of the polypeptides comprising combinations of the differentmotifs set forth in Table XIX, and/or, one or more of the predicted CTLepitopes of Table V through Table XVIII, and/or, one or more of the Tcell binding motifs known in the art. Preferred embodiments contain noinsertions, deletions or substitutions either within the motifs or theintervening sequences of the polypeptides. In addition, embodimentswhich include a number of either N-terminal and/or C-terminal amino acidresidues on either side of these motifs may be desirable (to, forexample, include a greater portion of the polypeptide architecture inwhich the motif is located). Typically the number of N-terminal and/orC-terminal amino acid residues on either side of a motif is betweenabout 1 to about 100 amino acid residues, preferably 5 to about 50 aminoacid residues.

238P1B2-related proteins are embodied in many forms, preferably inisolated form. A purified 238P1B2 protein molecule will be substantiallyfree of other proteins or molecules that impair the binding of 238P1B2to antibody, T cell or other ligand. The nature and degree of isolationand purification will depend on the intended use. Embodiments of a238P1B2-related proteins include purified 238P1B2-related proteins andfunctional, soluble 238P1B2-related proteins. In one embodiment, afunctional, soluble 238P1B2 protein or fragment thereof retains theability to be bound by antibody, T cell or other ligand.

The invention also provides 238P1B2 proteins comprising biologicallyactive fragments of a 238P1B2 amino acid sequence shown in FIG. 2 orFIG. 3. Such proteins exhibit properties of the starting 238P1B2protein, such as the ability to elicit the generation of antibodies thatspecifically bind an epitope associated with the starting 238P1B2protein; to be bound by such antibodies; to elicit the activation of HTLor CTL; and/or, to be recognized by HTL or CTL that also specificallybind to the starting protein.

238P1B2-related polypeptides that contain particularly interestingstructures can be predicted and/or identified using various analyticaltechniques well known in the art, including, for example, the methods ofChou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultzor Jameson-Wolf analysis, or on the basis of immunogenicity. Fragmentsthat contain such structures are particularly useful in generatingsubunit-specific anti-238P1B2 antibodies, or T cells or in identifyingcellular factors that bind to 238P1B2. For example, hydrophilicityprofiles can be generated, and immunogenic peptide fragments identified,using the method of Hopp, T. P. and Woods, K. R., 1981, Proc. Natl.Acad. Sci. U.S.A. 78:3824-3828. Hydropathicity profiles can begenerated, and immunogenic peptide fragments identified, using themethod of Kyte, J. and Doolittle, R. F., 1982, J. Mol. Biol.157:105-132. Percent (%) Accessible Residues profiles can be generated,and immunogenic peptide fragments identified, using the method of JaninJ., 1979, Nature 277:491-492. Average Flexibility profiles can begenerated, and immunogenic peptide fragments identified, using themethod of Bhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. ProteinRes. 32:242-255. Beta-turn profiles can be generated, and immunogenicpeptide fragments identified, using the method of Deleage, G., Roux B.,1987, Protein Engineering 1:289-294.

CTL epitopes can be determined using specific algorithms to identifypeptides within an 238P1B2 protein that are capable of optimally bindingto specified HLA alleles (e.g., by using the SYFPEITHI site; thelistings in Table IV(A)-(E); Epimatrix™ and Epimer™, Brown University,and BIMAS). Illustrating this, peptide epitopes from 238P1B2 that arepresented in the context of human MHC class I molecules HLA-A1, A2, A3,A11, A24, B7 and B35 were predicted (Tables V-XVIII, Table XIX).Specifically, the complete amino acid sequence of the 238P1B2 proteinand relevant portions of other variants, i.e., for HLA Class Ipredictions 9 flanking residues on either side of a point mutation, andfor HLA Class II predictions 14 flanking residues on either side of apoint mutation, were entered into the HLA Peptide Motif Search algorithmfound in the Bioinformatics and Molecular Analysis Section (BIMAS); inaddition to the site SYFPEITHI.

The HLA peptide motif search algorithm was developed by Dr. Ken Parkerbased on binding of specific peptide sequences in the groove of HLAClass I molecules, in particular HLA-A2 (see, e.g., Falk et al., Nature351: 290-6 (1991); Hunt et al., Science 255:1261-3 (1992); Parker etal., J. Immunol. 149:3580-7 (1992); Parker et al., J. Immunol.152:163-75 (1994)). This algorithm allows location and ranking of 8-mer,9-mer, and 10-mer peptides from a complete protein sequence forpredicted binding to HLA-A2 as well as numerous other HLA Class Imolecules. Many HLA class I binding peptides are 8-, 9-, 10 or 11-mers.For example, for class I HLA-A2, the epitopes preferably contain aleucine (L) or methionine (M) at position 2 and a valine (V) or leucine(L) at the C-terminus (see, e.g., Parker et al., J. Immunol. 149:3580-7(1992)). Selected results of 238P1B2 predicted binding peptides areshown in Tables V-XVIII and Table XIX herein. In Tables V-XVIII andTable XIX, selected candidates, 9-mers, 10-mers, and 15-mers for eachfamily member are shown along with their location, the amino acidsequence of each specific peptide, and an estimated binding score. Thebinding score corresponds to the estimated half time of dissociation ofcomplexes containing the peptide at 37° C. at pH 6.5. Peptides with thehighest binding score are predicted to be the most tightly bound to HLAClass I on the cell surface for the greatest period of time and thusrepresent the best immunogenic targets for T-cell recognition.

Actual binding of peptides to an HLA allele can be evaluated bystabilization of HLA expression on the antigen-processing defective cellline T2 (see, e.g., Xue et al., Prostate 30:73-8 (1997) and Peshwa etal., Prostate 36:129-38 (1998)). Immunogenicity of specific peptides canbe evaluated in vitro by stimulation of CD8+ cytotoxic T lymphocytes(CTL) in the presence of antigen presenting cells such as dendriticcells.

It is to be appreciated that every epitope predicted by the BIMAS site,Epimer™ and Epimatrix™ sites, or specified by the HLA class I or classII motifs available in the art or which become part of the art such asset forth in Table IV are to be “applied” to a 238P1B2 protein inaccordance with the invention. As used in this context “applied” meansthat a 238P1B2 protein is evaluated, e.g., visually or by computer-basedpatterns finding methods, as appreciated by those of skill in therelevant art. Every subsequence of a 238P1B2 protein of 8, 9, 10, or 11amino acid residues that bears an HLA Class I motif, or a subsequence of9 or more amino acid residues that bear an HLA Class II motif are withinthe scope of the invention.

III.B.) Expression of 238P1B2-Related Proteins

In an embodiment described in the examples that follow, 238P1B2 can beconveniently expressed in cells (such as 293T cells) transfected with acommercially available expression vector such as a CMV-driven expressionvector encoding 238P1B2 with a C-terminal 6× His and MYC tag(pcDNA3.1/mycHIS, Invitrogen or Tag5, GenHunter Corporation, NashvilleTenn.). The Tag5 vector provides an IgGK secretion signal that can beused to facilitate the production of a secreted 238P1B2 protein intransfected cells. The secreted HIS-tagged 238P1B2 in the culture mediacan be purified, e.g., using a nickel column using standard techniques.

III.C.) Modifications of 238P1B2-Related Proteins

Modifications of 238P1B2-related proteins such as covalent modificationsare included within the scope of this invention. One type of covalentmodification includes reacting targeted amino acid residues of a 238P1B2polypeptide with an organic derivatizing agent that is capable ofreacting with selected side chains or the N- or C-terminal residues of a238P1B2 protein. Another type of covalent modification of a 238P1B2polypeptide included within the scope of this invention comprisesaltering the native glycosylation pattern of a protein of the invention.Another type of covalent modification of 238P1B2 comprises linking a238P1B2 polypeptide to one of a variety of nonproteinaceous polymers,e.g., polyethylene glycol (PEG), polypropylene glycol, orpolyoxyalkylenes, in the manner set forth in U.S. Pat. No. 4,640,835;4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.

The 238P1B2-related proteins of the present invention can also bemodified to form a chimeric molecule comprising 238P1B2 fused toanother, heterologous polypeptide or amino acid sequence. Such achimeric molecule can be synthesized chemically or recombinantly. Achimeric molecule can have a protein of the invention fused to anothertumor-associated antigen or fragment thereof. Alternatively, a proteinin accordance with the invention can comprise a fusion of fragments of a238P1B2 sequence (amino or nucleic acid) such that a molecule is createdthat is not, through its length, directly homologous to the amino ornucleic acid sequences shown in FIG. 2 or FIG. 3. Such a chimericmolecule can comprise multiples of the same subsequence of 238P1B2. Achimeric molecule can comprise a fusion of a 238P1B2-related proteinwith a polyhistidine epitope tag, which provides an epitope to whichimmobilized nickel can selectively bind, with cytokines or with growthfactors. The epitope tag is generally placed at the amino- orcarboxyl-terminus of a 238P1B2 protein. In an alternative embodiment,the chimeric molecule can comprise a fusion of a 238P1B2-related proteinwith an immunoglobulin or a particular region of an immunoglobulin. Fora bivalent form of the chimeric molecule (also referred to as an“immunoadhesin”), such a fusion could be to the Fc region of an IgGmolecule. The Ig fusions preferably include the substitution of asoluble (transmembrane domain deleted or inactivated) form of a 238P1B2polypeptide in place of at least one variable region within an Igmolecule. In a preferred embodiment, the immunoglobulin fusion includesthe hinge, CH2 and CH3, or the hinge, CH1, CH2 and CH3 regions of anIgGI molecule. For the production of immunoglobulin fusions see, e.g.,U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.

III.D.) Uses of 238P1B2-Related Proteins

The proteins of the invention have a number of different specific uses.As 238P1B2 is highly expressed in prostate and other cancers,238P1B2-related proteins are used in methods that assess the status of238P1B2 gene products in normal versus cancerous tissues, therebyelucidating the malignant phenotype. Typically, polypeptides fromspecific regions of a 238P1B2 protein are used to assess the presence ofperturbations (such as deletions, insertions, point mutations etc.) inthose regions (such as regions containing one or more motifs). Exemplaryassays utilize antibodies or T cells targeting 238P1B2-related proteinscomprising the amino acid residues of one or more of the biologicalmotifs contained within a 238P1B2 polypeptide sequence in order toevaluate the characteristics of this region in normal versus canceroustissues or to elicit an immune response to the epitope. Alternatively,238P1B2-related proteins that contain the amino acid residues of one ormore of the biological motifs in a 238P1B2 protein are used to screenfor factors that interact with that region of 238P1B2.

238P1B2 protein fragments/subsequences are particularly useful ingenerating and characterizing domain-specific antibodies (e.g.,antibodies recognizing an extracellular or intracellular epitope of an238P1B2 protein), for identifying agents or cellular factors that bindto 238P1B2 or a particular structural domain thereof, and in varioustherapeutic and diagnostic contexts, including but not limited todiagnostic assays, cancer vaccines and methods of preparing suchvaccines.

Proteins encoded by the 238P1B2 genes, or by analogs, homologs orfragments thereof, have a variety of uses, including but not limited togenerating antibodies and in methods for identifying ligands and otheragents and cellular constituents that bind to an 238P1B2 gene product.Antibodies raised against an 238P1B2 protein or fragment thereof areuseful in diagnostic and prognostic assays, and imaging methodologies inthe management of human cancers characterized by expression of 238P1B2protein, such as those listed in Table I. Such antibodies can beexpressed intracellularly and used in methods of treating patients withsuch cancers. 238P1B2-related nucleic acids or proteins are also used ingenerating HTL or CTL responses.

Various immunological assays useful for the detection of 238P1B2proteins are used, including but not limited to various types ofradioimmunoassays, enzyme-linked immunosorbent assays (ELISA),enzyme-linked immunofluorescent assays (ELIFA), immunocytochemicalmethods, and the like. Antibodies can be labeled and used asimmunological imaging reagents capable of detecting 238P1B2-expressingcells (e.g., in radioscintigraphic imaging methods). 238P1B2 proteinsare also particularly useful in generating cancer vaccines, as furtherdescribed herein.

IV.) 238P1B2 Antibodies

Another aspect of the invention provides antibodies that bind to238P1B2-related proteins. Preferred antibodies specifically bind to a238P1B2-related protein and do not bind (or bind weakly) to peptides orproteins that are not 238P1B2-related proteins. For example, antibodiesthat bind 238P1B2 can bind 238P1B2-related proteins such as the homologsor analogs thereof.

238P1B2 antibodies of the invention are particularly useful in cancer(see, e.g., Table I) diagnostic and prognostic assays, and imagingmethodologies. Similarly, such antibodies are useful in the treatment,diagnosis, and/or prognosis of other cancers, to the extent 238P1B2 isalso expressed or overexpressed in these other cancers. Moreover,intracellularly expressed antibodies (e.g., single chain antibodies) aretherapeutically useful in treating cancers in which the expression of238P1B2 is involved, such as advanced or metastatic prostate cancers.

The invention also provides various immunological assays useful for thedetection and quantification of 238P1B2 and mutant 238P1B2-relatedproteins. Such assays can comprise one or more 238P1B2 antibodiescapable of recognizing and binding a 238P1B2-related protein, asappropriate. These assays are performed within various immunologicalassay formats well known in the art, including but not limited tovarious types of radioimmunoassays, enzyme-linked immunosorbent assays(ELISA), enzyme-linked immunofluorescent assays (ELIFA), and the like.

Immunological non-antibody assays of the invention also comprise T cellimmunogenicity assays (inhibitory or stimulatory) as well as majorhistocompatibility complex (MHC) binding assays.

In addition, immunological imaging methods capable of detecting prostatecancer and other cancers expressing 238P1B2 are also provided by theinvention, including but not limited to radioscintigraphic imagingmethods using labeled 238P1B2 antibodies. Such assays are clinicallyuseful in the detection, monitoring, and prognosis of 238P1B2 expressingcancers such as prostate cancer.

238P1B2 antibodies are also used in methods for purifying a238P1B2-related protein and for isolating 238P1B2 homologues and relatedmolecules. For example, a method of purifying a 238P1B2-related proteincomprises incubating an 238P1B2 antibody, which has been coupled to asolid matrix, with a lysate or other solution containing a238P1B2-related protein under conditions that permit the 238P1B2antibody to bind to the 238P1B2-related protein; washing the solidmatrix to eliminate impurities; and eluting the 238P1B2-related proteinfrom the coupled antibody. Other uses of 238P1B2 antibodies inaccordance with the invention include generating anti-idiotypicantibodies that mimic a 238P1B2 protein.

Various methods for the preparation of antibodies are well known in theart. For example, antibodies can be prepared by immunizing a suitablemammalian host using a 238P1B2-related protein, peptide, or fragment, inisolated or immunoconjugated form (Antibodies: A Laboratory Manual, CSHPress, Eds., Harlow, and Lane (1988); Harlow, Antibodies, Cold SpringHarbor Press, NY (1989)). In addition, fusion proteins of 238P1B2 canalso be used, such as a 238P1B2 GST-fusion protein. In a particularembodiment, a GST fusion protein comprising all or most of the aminoacid sequence of FIG. 2 or FIG. 3 is produced, then used as an immunogento generate appropriate antibodies. In another embodiment, a238P1B2-related protein is synthesized and used as an immunogen.

In addition, naked DNA immunization techniques known in the art are used(with or without purified 238P1B2-related protein or 238P1B2 expressingcells) to generate an immune response to the encoded immunogen (forreview, see Donnelly et al., 1997, Ann. Rev. Immunol. 15: 617-648).

The amino acid sequence of a 238P1B2 protein as shown in FIG. 2 or FIG.3 can be analyzed to select specific regions of the 238P1B2 protein forgenerating antibodies. For example, hydrophobicity and hydrophilicityanalyses of a 238P1B2 amino acid sequence are used to identifyhydrophilic regions in the 238P1B2 structure. Regions of a 238P1B2protein that show immunogenic structure, as well as other regions anddomains, can readily be identified using various other methods known inthe art, such as Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg,Karplus-Schultz or Jameson-Wolf analysis. Hydrophilicity profiles can begenerated using the method of Hopp, T. P. and Woods, K. R., 1981, Proc.Natl. Acad. Sci. U.S.A. 78:3824-3828. Hydropathicity profiles can begenerated using the method of Kyte, J. and Doolittle, R. F., 1982, J.Mol. Biol. 157:105-132. Percent (%) Accessible Residues profiles can begenerated using the method of Janin J., 1979, Nature 277:491-492.Average Flexibility profiles can be generated using the method ofBhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. Protein Res.32:242-255. Beta-turn profiles can be generated using the method ofDeleage, G., Roux B., 1987, Protein Engineering 1:289-294. Thus, eachregion identified by any of these programs or methods is within thescope of the present invention. Methods for the generation of 238P1B2antibodies are further illustrated by way of the examples providedherein. Methods for preparing a protein or polypeptide for use as animmunogen are well known in the art. Also well known in the art aremethods for preparing immunogenic conjugates of a protein with acarrier, such as BSA, KLH or other carrier protein. In somecircumstances, direct conjugation using, for example, carbodiimidereagents are used; in other instances linking reagents such as thosesupplied by Pierce Chemical Co., Rockford, Ill., are effective.Administration of a 238P1B2 immunogen is often conducted by injectionover a suitable time period and with use of a suitable adjuvant, as isunderstood in the art. During the immunization schedule, titers ofantibodies can be taken to determine adequacy of antibody formation.

238P1B2 monoclonal antibodies can be produced by various means wellknown in the art. For example, immortalized cell lines that secrete adesired monoclonal antibody are prepared using the standard hybridomatechnology of Kohler and Milstein or modifications that immortalizeantibody-producing B cells, as is generally known. Immortalized celllines that secrete the desired antibodies are screened by immunoassay inwhich the antigen is a 238P1B2-related protein. When the appropriateimmortalized cell culture is identified, the cells can be expanded andantibodies produced either from in vitro cultures or from ascites fluid.

The antibodies or fragments of the invention can also be produced, byrecombinant means. Regions that bind specifically to the desired regionsof a 238P1B2 protein can also be produced in the context of chimeric orcomplementarity determining region (CDR) grafted antibodies of multiplespecies origin. Humanized or human 238P1B2 antibodies can also beproduced, and are preferred for use in therapeutic contexts. Methods forhumanizing murine and other non-human antibodies, by substituting one ormore of the non-human antibody CDRs for corresponding human antibodysequences, are well known (see for example, Jones et al., 1986, Nature321: 522-525; Riechmann et al., 1988, Nature 332: 323-327; Verhoeyen etal., 1988, Science 239: 1534-1536). See also, Carter et al., 1993, Proc.Natl. Acad. Sci. USA 89: 4285 and Sims et al., 1993, J. Immunol. 151:2296.

Methods for producing fully human monoclonal antibodies include phagedisplay and transgenic methods (for review, see Vaughan et al., 1998,Nature Biotechnology 16: 535-539). Fully human 238P1B2 monoclonalantibodies can be generated using cloning technologies employing largehuman Ig gene combinatorial libraries (i.e., phage display) (Griffithsand Hoogenboom, Building an in vitro immune system: human antibodiesfrom phage display libraries. In: Protein Engineering of AntibodyMolecules for Prophylactic and Therapeutic Applications in Man, Clark,M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and Barbas, HumanAntibodies from combinatorial libraries. Id., pp 65-82). Fully human238P1B2 monoclonal antibodies can also be produced using transgenic miceengineered to contain human immunoglobulin gene loci as described in PCTPatent Application WO98/24893, Kucherlapati and Jakobovits et al.,published Dec. 3, 1997 (see also, Jakobovits, 1998, Exp. Opin. Invest.Drugs 7(4): 607-614; U.S. Pat. Nos. 6,162,963 issued 19 Dec. 2000;6,150,584 issued 12 Nov. 2000; and, 6,114,598 issued 5 Sep. 2000). Thismethod avoids the in vitro manipulation required with phage displaytechnology and efficiently produces high affinity authentic humanantibodies.

Reactivity of 238P1B2 antibodies with an 238P1B2-related protein can beestablished by a number of well known means, including Western blot,immunoprecipitation, ELISA, and FACS analyses using, as appropriate,238P1B2-related proteins, 238P1B2-expressing cells or extracts thereof.A 238P1B2 antibody or fragment thereof can be labeled with a detectablemarker or conjugated to a second molecule. Suitable detectable markersinclude, but are not limited to, a radioisotope, a fluorescent compound,a bioluminescent compound, chemiluminescent compound, a metal chelatoror an enzyme. Further, bi-specific antibodies specific for two or more238P1B2 epitopes are generated using methods generally known in the art.Homodimeric antibodies can also be generated by cross-linking techniquesknown in the art (e.g., Wolff et al., Cancer Res. 53: 2560-2565).

V.) 238P1B2 Cellular Immune Responses

The mechanism by which T cells recognize antigens has been delineated.Efficacious peptide epitope vaccine compositions of the invention inducea therapeutic or prophylactic immune responses in very broad segments ofthe world-wide population. For an understanding of the value andefficacy of compositions of the invention that induce cellular immuneresponses, a brief review of immunology-related technology is provided.

A complex of an HLA molecule and a peptidic antigen acts as the ligandrecognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071,1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. andBodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev.Immunol. 11:403, 1993). Through the study of single amino acidsubstituted antigen analogs and the sequencing of endogenously bound,naturally processed peptides, critical residues that correspond tomotifs required for specific binding to HLA antigen molecules have beenidentified and are set forth in Table IV (see also, e.g., Southwood, etal., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics41:178, 1995; Rammensee et al., SYFPEITHI; Sette, A. and Sidney, J.Curr. Opin. Immunol. 10:478, 1998; Engelhard, V. H., Curr. Opin.Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol.4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994;Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol.155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996;Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J.Immunogenetics 1999 November; 50(3-4):201-12, Review).

Furthermore, x-ray crystallographic analyses of HLA-peptide complexeshave revealed pockets within the peptide binding cleft/groove of HLAmolecules which accommodate, in an allele-specific mode, residues borneby peptide ligands; these residues in turn determine the HLA bindingcapacity of the peptides in which they are present. (See, e.g., Madden,D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203,1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H.et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci.USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M.L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927,1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D.C., J. Mol.Biol. 219:277, 1991.)

Accordingly, the definition of class I and class II allele-specific HLAbinding motifs, or class I or class II supermotifs allows identificationof regions within a protein that are correlated with binding toparticular HLA antigen(s).

Thus, by a process of HLA motif identification, candidates forepitope-based vaccines have been identified; such candidates can befurther evaluated by HLA-peptide binding assays to determine bindingaffinity and/or the time period of association of the epitope and itscorresponding HLA molecule. Additional confirmatory work can beperformed to select, amongst these vaccine candidates, epitopes withpreferred characteristics in terms of population coverage, and/orimmunogenicity.

Various strategies can be utilized to evaluate cellular immunogenicity,including:

1) Evaluation of primary T cell cultures from normal individuals (see,e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. etal., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J.Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1,1998). This procedure involves the stimulation of peripheral bloodlymphocytes (PBL) from normal subjects with a test peptide in thepresence of antigen presenting cells in vitro over a period of severalweeks. T cells specific for the peptide become activated during thistime and are detected using, e.g., a lymphokine- or ⁵¹Cr-release assayinvolving peptide sensitized target cells.

2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. etal., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol.8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997). Forexample, in such methods peptides in incomplete Freund's adjuvant areadministered subcutaneously to HLA transgenic mice. Several weeksfollowing immunization, splenocytes are removed and cultured in vitro inthe presence of test peptide for approximately one week.Peptide-specific T cells are detected using, e.g., a ⁵¹Cr-release assayinvolving peptide sensitized target cells and target cells expressingendogenously generated antigen.

3) Demonstration of recall T cell responses from immune individuals whohave been either effectively vaccinated and/or from chronically illpatients (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995;Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin.Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648,1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). Accordingly,recall responses are detected by culturing PBL from subjects that havebeen exposed to the antigen due to disease and thus have generated animmune response “naturally”, or from patients who were vaccinatedagainst the antigen. PBL from subjects are cultured in vitro for 1-2weeks in the presence of test peptide plus antigen presenting cells(APC) to allow activation of “memory” T cells, as compared to “naive” Tcells. At the end of the culture period, T cell activity is detectedusing assays including ⁵¹Cr release involving peptide-sensitizedtargets, T cell proliferation, or lymphokine release.

VI.) 238P1B2 Transgenic Animals

Nucleic acids that encode a 238P1B2-related protein can also be used togenerate either transgenic animals or “knock out” animals that, in turn,are useful in the development and screening of therapeutically usefulreagents. In accordance with established techniques, cDNA encoding238P1B2 can be used to clone genomic DNA that encodes 238P1B2. Thecloned genomic sequences can then be used to generate transgenic animalscontaining cells that express DNA that encode 238P1B2. Methods forgenerating transgenic animals, particularly animals such as mice orrats, have become conventional in the art and are described, forexample, in U.S. Pat. Nos. 4,736,866 issued 12 Apr. 1988, and 4,870,009issued 26 Sep. 1989. Typically, particular cells would be targeted for238P1B2 transgene incorporation with tissue-specific enhancers.

Transgenic animals that include a copy of a transgene encoding 238P1B2can be used to examine the effect of increased expression of DNA thatencodes 238P1B2. Such animals can be used as tester animals for reagentsthought to confer protection from, for example, pathological conditionsassociated with its overexpression. In accordance with this aspect ofthe invention, an animal is treated with a reagent and a reducedincidence of a pathological condition, compared to untreated animalsthat bear the transgene, would indicate a potential therapeuticintervention for the pathological condition.

Alternatively, non-human homologues of 238P1B2 can be used to constructa 238P1B2 “knock out” animal that has a defective or altered geneencoding 238P1B2 as a result of homologous recombination between theendogenous gene encoding 238P1B2 and altered genomic DNA encoding238P1B2 introduced into an embryonic cell of the animal. For example,cDNA that encodes 238P1B2 can be used to clone genomic DNA encoding238P1B2 in accordance with established techniques. A portion of thegenomic DNA encoding 238P1B2 can be deleted or replaced with anothergene, such as a gene encoding a selectable marker that can be used tomonitor integration. Typically, several kilobases of unaltered flankingDNA (both at the 5′ and 3′ ends) are included in the vector (see, e.g.,Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologousrecombination vectors). The vector is introduced into an embryonic stemcell line (e.g., by electroporation) and cells in which the introducedDNA has homologously recombined with the endogenous DNA are selected(see, e.g., Li et al., Cell, 69:915 (1992)). The selected cells are theninjected into a blastocyst of an animal (e.g., a mouse or rat) to formaggregation chimeras (see, e.g., Bradley, in Teratocarcinomas andEmbryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL,Oxford, 1987), pp. 113-152). A chimeric embryo can then be implantedinto a suitable pseudopregnant female foster animal, and the embryobrought to term to create a “knock out” animal. Progeny harboring thehomologously recombined DNA in their germ cells can be identified bystandard techniques and used to breed animals in which all cells of theanimal contain the homologously recombined DNA. Knock out animals can becharacterized, for example, for their ability to defend against certainpathological conditions or for their development of pathologicalconditions due to absence of a 238P1B2 polypeptide.

VII.) Methods for the Detection of 238P1B2

Another aspect of the present invention relates to methods for detecting238P1B2 polynucleotides and 238P1B2-related proteins, as well as methodsfor identifying a cell that expresses 238P1B2. The expression profile of238P1B2 makes it a diagnostic marker for metastasized disease.Accordingly, the status of 238P1B2 gene products provides informationuseful for predicting a variety of factors including susceptibility toadvanced stage disease, rate of progression, and/or tumoraggressiveness. As discussed in detail herein, the status of 238P1B2gene products in patient samples can be analyzed by a variety protocolsthat are well known in the art including immunohistochemical analysis,the variety of Northern blotting techniques including in situhybridization, RT-PCR analysis (for example on laser capturemicro-dissected samples), Western blot analysis and tissue arrayanalysis.

More particularly, the invention provides assays for the detection of238P1B2 polynucleotides in a biological sample, such as serum, bone,prostate, and other tissues, urine, semen, cell preparations, and thelike. Detectable 238P1B2 polynucleotides include, for example, a 238P1B2gene or fragment thereof, 238P1B2 mRNA, alternative splice variant238P1B2 mRNAs, and recombinant DNA or RNA molecules that contain a238P1B2 polynucleotide. A number of methods for amplifying and/ordetecting the presence of 238P1B2 polynucleotides are well known in theart and can be employed in the practice of this aspect of the invention.

In one embodiment, a method for detecting an 238P1B2 mRNA in abiological sample comprises producing cDNA from the sample by reversetranscription using at least one primer; amplifying the cDNA so producedusing an 238P1B2 polynucleotides as sense and antisense primers toamplify 238P1B2 cDNAs therein; and detecting the presence of theamplified 238P1B2 cDNA. Optionally, the sequence of the amplified238P1B2 cDNA can be determined.

In another embodiment, a method of detecting a 238P1B2 gene in abiological sample comprises first isolating genomic DNA from the sample;amplifying the isolated genomic DNA using 238P1B2 polynucleotides assense and antisense primers; and detecting the presence of the amplified238P1B2 gene. Any number of appropriate sense and antisense probecombinations can be designed from a 238P1B2 nucleotide sequence (see,e.g., FIG. 2) and used for this purpose.

The invention also provides assays for detecting the presence of an238P1B2 protein in a tissue or other biological sample such as serum,semen, bone, prostate, urine, cell preparations, and the like. Methodsfor detecting a 238P1B2-related protein are also well known and include,for example, immunoprecipitation, immunohistochemical analysis, Westernblot analysis, molecular binding assays, ELISA, ELIFA and the like. Forexample, a method of detecting the presence of a 238P1B2-related proteinin a biological sample comprises first contacting the sample with a238P1B2 antibody, a 238P1B2-reactive fragment thereof, or a recombinantprotein containing an antigen binding region of a 238P1B2 antibody; andthen detecting the binding of 238P1B2-related protein in the sample.

Methods for identifying a cell that expresses 238P1B2 are also withinthe scope of the invention. In one embodiment, an assay for identifyinga cell that expresses a 238P1B2 gene comprises detecting the presence of238P1B2 mRNA in the cell. Methods for the detection of particular mRNAsin cells are well known and include, for example, hybridization assaysusing complementary DNA probes (such as in situ hybridization usinglabeled 238P1B2 riboprobes, Northern blot and related techniques) andvarious nucleic acid amplification assays (such as RT-PCR usingcomplementary primers specific for 238P1B2, and other amplification typedetection methods, such as, for example, branched DNA, SISBA, TMA andthe like). Alternatively, an assay for identifying a cell that expressesa 238P1B2 gene comprises detecting the presence of 238P1B2-relatedprotein in the cell or secreted by the cell. Various methods for thedetection of proteins are well known in the art and are employed for thedetection of 238P1B2-related proteins and cells that express238P1B2-related proteins.

238P1B2 expression analysis is also useful as a tool for identifying andevaluating agents that modulate 238P1B2 gene expression. For example,238P1B2 expression is significantly upregulated in prostate cancer, andis expressed in cancers of the tissues listed in Table I. Identificationof a molecule or biological agent that inhibits 238P1B2 expression orover-expression in cancer cells is of therapeutic value. For example,such an agent can be identified by using a screen that quantifies238P1B2 expression by RT-PCR, nucleic acid hybridization or antibodybinding.

VIII.) Methods for Monitoring the Status of 238P1B2-Related Genes andtheir Products

Oncogenesis is known to be a multistep process where cellular growthbecomes progressively dysregulated and cells progress from a normalphysiological state to precancerous and then cancerous states (see,e.g., Alers et al., Lab Invest. 77(5): 437-438 (1997) and Isaacs et al.,Cancer Surv. 23: 19-32 (1995)). In this context, examining a biologicalsample for evidence of dysregulated cell growth (such as aberrant238P1B2 expression in cancers) allows for early detection of suchaberrant physiology, before a pathologic state such as cancer hasprogressed to a stage that therapeutic options are more limited and orthe prognosis is worse. In such examinations, the status of 238P1B2 in abiological sample of interest can be compared, for example, to thestatus of 238P1B2 in a corresponding normal sample (e.g. a sample fromthat individual or alternatively another individual that is not affectedby a pathology). An alteration in the status of 238P1B2 in thebiological sample (as compared to the normal sample) provides evidenceof dysregulated cellular growth. In addition to using a biologicalsample that is not affected by a pathology as a normal sample, one canalso use a predetermined normative value such as a predetermined normallevel of mRNA expression (see, e.g., Grever et al., J. Comp. Neurol.1996 Dec. 9; 376(2): 306-14 and U.S. Pat. No. 5,837,501) to compare238P1B2 status in a sample.

The term “status” in this context is used according to its art acceptedmeaning and refers to the condition or state of a gene and its products.Typically, skilled artisans use a number of parameters to evaluate thecondition or state of a gene and its products. These include, but arenot limited to the location of expressed gene products (including thelocation of 238P1B2 expressing cells) as well as the level, andbiological activity of expressed gene products (such as 238P1B2 mRNA,polynucleotides and polypeptides). Typically, an alteration in thestatus of 238P1B2 comprises a change in the location of 238P1B2 and/or238P1B2 expressing cells and/or an increase in 238P1B2 mRNA and/orprotein expression.

238P1B2 status in a sample can be analyzed by a number of means wellknown in the art, including without limitation, immunohistochemicalanalysis, in situ hybridization, RT-PCR analysis on laser capturemicro-dissected samples, Western blot analysis, and tissue arrayanalysis. Typical protocols for evaluating the status of a 238P1B2 geneand gene products are found, for example in Ausubel et al. eds., 1995,Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4(Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Thus,the status of 238P1B2 in a biological sample is evaluated by variousmethods utilized by skilled artisans including, but not limited togenomic Southern analysis (to examine, for example perturbations in a238P1B2 gene), Northern analysis and/or PCR analysis of 238P1B2 mRNA (toexamine, for example alterations in the polynucleotide sequences orexpression levels of 238P1B2 mRNAs), and, Western and/orimmunohistochemical analysis (to examine, for example alterations inpolypeptide sequences, alterations in polypeptide localization within asample, alterations in expression levels of 238P1B2 proteins and/orassociations of 238P1B2 proteins with polypeptide binding partners).Detectable 238P1B2 polynucleotides include, for example, a 238P1B2 geneor fragment thereof, 238P1B2 mRNA, alternative splice variants, 238P1B2mRNAs, and recombinant DNA or RNA molecules containing a 238P1B2polynucleotide.

The expression profile of 238P1B2 makes it a diagnostic marker for localand/or metastasized disease, and provides information on the growth oroncogenic potential of a biological sample. In particular, the status of238P1B2 provides information useful for predicting susceptibility toparticular disease stages, progression, and/or tumor aggressiveness. Theinvention provides methods and assays for determining 238P1B2 status anddiagnosing cancers that express 238P1B2, such as cancers of the tissueslisted in Table I. For example, because 238P1B2 mRNA is so highlyexpressed in prostate and other cancers relative to normal prostatetissue, assays that evaluate the levels of 238P1B2 mRNA transcripts orproteins in a biological sample can be used to diagnose a diseaseassociated with 238P1B2 dysregulation, and can provide prognosticinformation useful in defining appropriate therapeutic options.

The expression status of 238P1B2 provides information including thepresence, stage and location of dysplastic, precancerous and cancerouscells, predicting susceptibility to various stages of disease, and/orfor gauging tumor aggressiveness. Moreover, the expression profile makesit useful as an imaging reagent for metastasized disease. Consequently,an aspect of the invention is directed to the various molecularprognostic and diagnostic methods for examining the status of 238P1B2 inbiological samples such as those from individuals suffering from, orsuspected of suffering from a pathology characterized by dysregulatedcellular growth, such as cancer.

As described above, the status of 238P1B2 in a biological sample can beexamined by a number of well-known procedures in the art. For example,the status of 238P1B2 in a biological sample taken from a specificlocation in the body can be examined by evaluating the sample for thepresence or absence of 238P1B2 expressing cells (e.g. those that express238P1B2 mRNAs or proteins). This examination can provide evidence ofdysregulated cellular growth, for example, when 238P1B2-expressing cellsare found in a biological sample that does not normally contain suchcells (such as a lymph node), because such alterations in the status of238P1B2 in a biological sample are often associated with dysregulatedcellular growth. Specifically, one indicator of dysregulated cellulargrowth is the metastases of cancer cells from an organ of origin (suchas the prostate) to a different area of the body (such as a lymph node).In this context, evidence of dysregulated cellular growth is importantfor example because occult lymph node metastases can be detected in asubstantial proportion of patients with prostate cancer, and suchmetastases are associated with known predictors of disease progression(see, e.g., Murphy et al., Prostate 42(4): 315-317 (2000); Su et al.,Semin. Surg. Oncol. 18(1): 17-28 (2000) and Freeman et al., J Urol 1995August 154(2 Pt 1):474-8).

In one aspect, the invention provides methods for monitoring 238P1B2gene products by determining the status of 238P1B2 gene productsexpressed by cells from an individual suspected of having a diseaseassociated with dysregulated cell growth (such as hyperplasia or cancer)and then comparing the status so determined to the status of 238P1B2gene products in a corresponding normal sample. The presence of aberrant238P1B2 gene products in the test sample relative to the normal sampleprovides an indication of the presence of dysregulated cell growthwithin the cells of the individual.

In another aspect, the invention provides assays useful in determiningthe presence of cancer in an individual, comprising detecting asignificant increase in 238P1B2 mRNA or protein expression in a testcell or tissue sample relative to expression levels in the correspondingnormal cell or tissue. The presence of 238P1B2 mRNA can, for example, beevaluated in tissue samples including but not limited to those listed inTable I. The presence of significant 238P1B2 expression in any of thesetissues is useful to indicate the emergence, presence and/or severity ofa cancer, since the corresponding normal tissues do not express 238P1B2mRNA or express it at lower levels.

In a related embodiment, 238P1B2 status is determined at the proteinlevel rather than at the nucleic acid level. For example, such a methodcomprises determining the level of 238P1B2 protein expressed by cells ina test tissue sample and comparing the level so determined to the levelof 238P1B2 expressed in a corresponding normal sample. In oneembodiment, the presence of 238P1B2 protein is evaluated, for example,using immunohistochemical methods. 238P1B2 antibodies or bindingpartners capable of detecting 238P1B2 protein expression are used in avariety of assay formats well known in the art for this purpose.

In a further embodiment, one can evaluate the status of 238P1B2nucleotide and amino acid sequences in a biological sample in order toidentify perturbations in the structure of these molecules. Theseperturbations can include insertions, deletions, substitutions and thelike. Such evaluations are useful because perturbations in thenucleotide and amino acid sequences are observed in a large number ofproteins associated with a growth dysregulated phenotype (see, e.g.,Marrogi et al., 1999, J. Cutan. Pathol. 26(8):369-378). For example, amutation in the sequence of 238P1B2 may be indicative of the presence orpromotion of a tumor. Such assays therefore have diagnostic andpredictive value where a mutation in 238P1B2 indicates a potential lossof function or increase in tumor growth.

A wide variety of assays for observing perturbations in nucleotide andamino acid sequences are well known in the art. For example, the sizeand structure of nucleic acid or amino acid sequences of 238P1B2 geneproducts are observed by the Northern, Southern, Western, PCR and DNAsequencing protocols discussed herein. In addition, other methods forobserving perturbations in nucleotide and amino acid sequences such assingle strand conformation polymorphism analysis are well known in theart (see, e.g., U.S. Pat. Nos. 5,382,510 issued 7 Sep. 1999, and5,952,170 issued 17 Jan. 1995).

Additionally, one can examine the methylation status of a 238P1B2 genein a biological sample. Aberrant demethylation and/or hypermethylationof CpG islands in gene 5′ regulatory regions frequently occurs inimmortalized and transformed cells, and can result in altered expressionof various genes. For example, promoter hypermethylation of the pi-classglutathione S-transferase (a protein expressed in normal prostate butnot expressed in >90% of prostate carcinomas) appears to permanentlysilence transcription of this gene and is the most frequently detectedgenomic alteration in prostate carcinomas (De Marzo et al., Am. J.Pathol. 155(6): 1985-1992 (1999)). In addition, this alteration ispresent in at least 70% of cases of high-grade prostatic intraepithelialneoplasia (PIN) (Brooks et al., Cancer Epidemiol. Biomarkers Prev.,1998, 7:531-536). In another example, expression of the LAGE-I tumorspecific gene (which is not expressed in normal prostate but isexpressed in 25-50% of prostate cancers) is induced by deoxy-azacytidinein lymphoblastoid cells, suggesting that tumoral expression is due todemethylation (Lethe et al., Int. J. Cancer 76(6): 903-908 (1998)). Avariety of assays for examining methylation status of a gene are wellknown in the art. For example, one can utilize, in Southernhybridization approaches, methylation-sensitive restriction enzymes thatcannot cleave sequences that contain methylated CpG sites to assess themethylation status of CpG islands. In addition, MSP (methylationspecific PCR) can rapidly profile the methylation status of all the CpGsites present in a CpG island of a given gene. This procedure involvesinitial modification of DNA by sodium bisulfite (which will convert allunmethylated cytosines to uracil) followed by amplification usingprimers specific for methylated versus unmethylated DNA. Protocolsinvolving methylation interference can also be found for example inCurrent Protocols In Molecular Biology, Unit 12, Frederick M. Ausubel etal. eds., 1995.

Gene amplification is an additional method for assessing the status of238P1B2. Gene amplification is measured in a sample directly, forexample, by conventional Southern blotting or Northern blotting toquantitate the transcription of mRNA (Thomas, 1980, Proc. Natl. Acad.Sci. USA, 77:5201-5205), dot blotting (DNA analysis), or in situhybridization, using an appropriately labeled probe, based on thesequences provided herein. Alternatively, antibodies are employed thatrecognize specific duplexes, including DNA duplexes, RNA duplexes, andDNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turnare labeled and the assay carried out where the duplex is bound to asurface, so that upon the formation of duplex on the surface, thepresence of antibody bound to the duplex can be detected.

Biopsied tissue or peripheral blood can be conveniently assayed for thepresence of cancer cells using for example, Northern, dot blot or RT-PCRanalysis to detect 238P1B2 expression. The presence of RT-PCRamplifiable 238P1B2 mRNA provides an indication of the presence ofcancer. RT-PCR assays are well known in the art. RT-PCR detection assaysfor tumor cells in peripheral blood are currently being evaluated foruse in the diagnosis and management of a number of human solid tumors.In the prostate cancer field, these include RT-PCR assays for thedetection of cells expressing PSA and PSM (Verkaik et al., 1997, Urol.Res. 25:373-384; Ghossein et al., 1995, J. Clin. Oncol. 13:1195-2000;Heston et al., 1995, Clin. Chem. 41:1687-1688).

A further aspect of the invention is an assessment of the susceptibilitythat an individual has for developing cancer. In one embodiment, amethod for predicting susceptibility to cancer comprises detecting238P1B2 mRNA or 238P1B2 protein in a tissue sample, its presenceindicating susceptibility to cancer, wherein the degree of 238P1B2 mRNAexpression correlates to the degree of susceptibility. In a specificembodiment, the presence of 238P1B2 in prostate or other tissue isexamined, with the presence of 238P1B2 in the sample providing anindication of prostate cancer susceptibility (or the emergence orexistence of a prostate tumor). Similarly, one can evaluate theintegrity 238P1B2 nucleotide and amino acid sequences in a biologicalsample, in order to identify perturbations in the structure of thesemolecules such as insertions, deletions, substitutions and the like. Thepresence of one or more perturbations in 238P1B2 gene products in thesample is an indication of cancer susceptibility (or the emergence orexistence of a tumor).

The invention also comprises methods for gauging tumor aggressiveness.In one embodiment, a method for gauging aggressiveness of a tumorcomprises determining the level of 238P1B2 mRNA or 238P1B2 proteinexpressed by tumor cells, comparing the level so determined to the levelof 238P1B2 mRNA or 238P1B2 protein expressed in a corresponding normaltissue taken from the same individual or a normal tissue referencesample, wherein the degree of 238P1B2 mRNA or 238P1B2 protein expressionin the tumor sample relative to the normal sample indicates the degreeof aggressiveness. In a specific embodiment, aggressiveness of a tumoris evaluated by determining the extent to which 238P1B2 is expressed inthe tumor cells, with higher expression levels indicating moreaggressive tumors. Another embodiment is the evaluation of the integrityof 238P1B2 nucleotide and amino acid sequences in a biological sample,in order to identify perturbations in the structure of these moleculessuch as insertions, deletions, substitutions and the like. The presenceof one or more perturbations indicates more aggressive tumors.

Another embodiment of the invention is directed to methods for observingthe progression of a malignancy in an individual over time. In oneembodiment, methods for observing the progression of a malignancy in anindividual over time comprise determining the level of 238P1B2 mRNA or238P1B2 protein expressed by cells in a sample of the tumor, comparingthe level so determined to the level of 238P1B2 mRNA or 238P1B2 proteinexpressed in an equivalent tissue sample taken from the same individualat a different time, wherein the degree of 238P1B2 mRNA or 238P1B2protein expression in the tumor sample over time provides information onthe progression of the cancer. In a specific embodiment, the progressionof a cancer is evaluated by determining 238P1B2 expression in the tumorcells over time, where increased expression over time indicates aprogression of the cancer. Also, one can evaluate the integrity 238P1B2nucleotide and amino acid sequences in a biological sample in order toidentify perturbations in the structure of these molecules such asinsertions, deletions, substitutions and the like, where the presence ofone or more perturbations indicates a progression of the cancer.

The above diagnostic approaches can be combined with any one of a widevariety of prognostic and diagnostic protocols known in the art. Forexample, another embodiment of the invention is directed to methods forobserving a coincidence between the expression of 238P1B2 gene and238P1B2 gene products (or perturbations in 238P1B2 gene and 238P1B2 geneproducts) and a factor that is associated with malignancy, as a meansfor diagnosing and prognosticating the status of a tissue sample. A widevariety of factors associated with malignancy can be utilized, such asthe expression of genes associated with malignancy (e.g. PSA, PSCA andPSM expression for prostate cancer etc.) as well as gross cytologicalobservations (see, e.g., Bocking et al., 1984, Anal. Quant. Cytol.6(2):74-88; Epstein, 1995, Hum. Pathol. 26(2):223-9; Thorson et al.,1998, Mod. Pathol. 11(6):543-51; Baisden et al., 1999, Am. J. Surg.Pathol. 23(8):918-24). Methods for observing a coincidence between theexpression of 238P1B2 gene and 238P1B2 gene products (or perturbationsin 238P1B2 gene and 238P1B2 gene products) and another factor that isassociated with malignancy are useful, for example, because the presenceof a set of specific factors that coincide with disease providesinformation crucial for diagnosing and prognosticating the status of atissue sample.

In one embodiment, methods for observing a coincidence between theexpression of 238P1B2 gene and 238P1B2 gene products (or perturbationsin 238P1B2 gene and 238P1B2 gene products) and another factor associatedwith malignancy entails detecting the overexpression of 238P1B2 mRNA orprotein in a tissue sample, detecting the overexpression of PSA mRNA orprotein in a tissue sample (or PSCA or PSM expression), and observing acoincidence of 238P1B2 mRNA or protein and PSA mRNA or proteinoverexpression (or PSCA or PSM expression). In a specific embodiment,the expression of 238P1B2 and PSA mRNA in prostate tissue is examined,where the coincidence of 238P1B2 and PSA mRNA overexpression in thesample indicates the existence of prostate cancer, prostate cancersusceptibility or the emergence or status of a prostate tumor.

Methods for detecting and quantifying the expression of 238P1B2 mRNA orprotein are described herein, and standard nucleic acid and proteindetection and quantification technologies are well known in the art.Standard methods for the detection and quantification of 238P1B2 mRNAinclude in situ hybridization using labeled 238P1B2 riboprobes, Northernblot and related techniques using 238P1B2 polynucleotide probes, RT-PCRanalysis using primers specific for 238P1B2, and other amplificationtype detection methods, such as, for example, branched DNA, SISBA, TMAand the like. In a specific embodiment, semi-quantitative RT-PCR is usedto detect and quantify 238P1B2 mRNA expression. Any number of primerscapable of amplifying 238P1B2 can be used for this purpose, includingbut not limited to the various primer sets specifically describedherein. In a specific embodiment, polyclonal or monoclonal antibodiesspecifically reactive with the wild-type 238P1B2 protein can be used inan immunohistochemical assay of biopsied tissue.

IX.) Identification of Molecules that Interact with 238P1B2

The 238P1B2 protein and nucleic acid sequences disclosed herein allow askilled artisan to identify proteins, small molecules and other agentsthat interact with 238P1B2, as well as pathways activated by 238P1B2 viaany one of a variety of art accepted protocols. For example, one canutilize one of the so-called interaction trap systems (also referred toas the “two-hybrid assay”). In such systems, molecules interact andreconstitute a transcription factor which directs expression of areporter gene, whereupon the expression of the reporter gene is assayed.Other systems identify protein-protein interactions in vivo throughreconstitution of a eukaryotic transcriptional activator, see, e.g.,U.S. Pat. Nos. 5,955,280 issued 21 Sep. 1999, 5,925,523 issued 20 Jul.1999, 5,846,722 issued 8 Dec. 1998 and 6,004,746 issued 21 Dec. 1999.Algorithms are also available in the art for genome-based predictions ofprotein function (see, e.g., Marcotte, et al., Nature 402: 4 Nov. 1999,83-86).

Alternatively one can screen peptide libraries to identify moleculesthat interact with 238P1B2 protein sequences. In such methods, peptidesthat bind to 238P1B2 are identified by screening libraries that encode arandom or controlled collection of amino acids. Peptides encoded by thelibraries are expressed as fusion proteins of bacteriophage coatproteins, the bacteriophage particles are then screened against the238P1B2 protein(s).

Accordingly, peptides having a wide variety of uses, such astherapeutic, prognostic or diagnostic reagents, are thus identifiedwithout any prior information on the structure of the expected ligand orreceptor molecule. Typical peptide libraries and screening methods thatcan be used to identify molecules that interact with 238P1B2 proteinsequences are disclosed for example in U.S. Pat. Nos. 5,723,286 issued 3Mar. 1998 and 5,733,731 issued 31 Mar. 1998.

Alternatively, cell lines that express 238P1B2 are used to identifyprotein-protein interactions mediated by 238P1B2. Such interactions canbe examined using immunoprecipitation techniques (see, e.g., Hamilton B.J., et al. Biochem. Biophys. Res. Commun. 1999, 261:646-51). 238P1B2protein can be immunoprecipitated from 238P1B2-expressing cell linesusing anti-238P1B2 antibodies. Alternatively, antibodies against His-tagcan be used in a cell line engineered to express fusions of 238P1B2 anda His-tag (vectors mentioned above). The immunoprecipitated complex canbe examined for protein association by procedures such as Westernblotting, ³⁵S-methionine labeling of proteins, protein microsequencing,silver staining and two-dimensional gel electrophoresis.

Small molecules and ligands that interact with 238P1B2 can be identifiedthrough related embodiments of such screening assays. For example, smallmolecules can be identified that interfere with protein function,including molecules that interfere with 238P1B2's ability to mediatephosphorylation and de-phosphorylation, interaction with DNA or RNAmolecules as an indication of regulation of cell cycles, secondmessenger signaling or tumorigenesis. Similarly, small molecules thatmodulate 238P1B2-related ion channel, protein pump, or cellcommunication functions are identified and used to treat patients thathave a cancer that expresses 238P1B2 (see, e.g., Hille, B., IonicChannels of Excitable Membranes 2^(nd) Ed., Sinauer Assoc., Sunderland,Mass., 1992). Moreover, ligands that regulate 238P1B2 function can beidentified based on their ability to bind 238P1B2 and activate areporter construct. Typical methods are discussed for example in U.S.Pat. No. 5,928,868 issued 27 Jul. 1999, and include methods for forminghybrid ligands in which at least one ligand is a small molecule. In anillustrative embodiment, cells engineered to express a fusion protein of238P1B2 and a DNA-binding protein are used to co-express a fusionprotein of a hybrid ligand/small molecule and a cDNA librarytranscriptional activator protein. The cells further contain a reportergene, the expression of which is conditioned on the proximity of thefirst and second fusion proteins to each other, an event that occursonly if the hybrid ligand binds to target sites on both hybrid proteins.Those cells that express the reporter gene are selected and the unknownsmall molecule or the unknown ligand is identified. This method providesa means of identifying modulators which activate or inhibit 238P1B2.

An embodiment of this invention comprises a method of screening for amolecule that interacts with an 238P1B2 amino acid sequence shown inFIG. 2 or FIG. 3, comprising the steps of contacting a population ofmolecules with a 238P1B2 amino acid sequence, allowing the population ofmolecules and the 238P1B2 amino acid sequence to interact underconditions that facilitate an interaction, determining the presence of amolecule that interacts with the 238P1B2 amino acid sequence, and thenseparating molecules that do not interact with the 238P1B2 amino acidsequence from molecules that do. In a specific embodiment, the methodfurther comprises purifying, characterizing and identifying a moleculethat interacts with the 238P1B2 amino acid sequence. The identifiedmolecule can be used to modulate a function performed by 238P1B2. In apreferred embodiment, the 238P1B2 amino acid sequence is contacted witha library of peptides.

X.) Therapeutic Methods and Compositions

The identification of 238P1B2 as a protein that is normally expressed ina restricted set of tissues, but which is also expressed in prostate andother cancers, opens a number of therapeutic approaches to the treatmentof such cancers. As contemplated herein, 238P1B2 functions as atranscription factor involved in activating tumor-promoting genes orrepressing genes that block tumorigenesis.

Accordingly, therapeutic approaches that inhibit the activity of a238P1B2 protein are useful for patients suffering from a cancer thatexpresses 238P1B2. These therapeutic approaches generally fall into twoclasses. One class comprises various methods for inhibiting the bindingor association of a 238P1B2 protein with its binding partner or withother proteins. Another class comprises a variety of methods forinhibiting the transcription of a 238P1B2 gene or translation of 238P1B2mRNA.

X.A.) Anti-Cancer Vaccines

The invention provides cancer vaccines comprising a 238P1B2-relatedprotein or 238P1B2-related nucleic acid. In view of the expression of238P1B2, cancer vaccines prevent and/or treat 238P1B2-expressing cancerswith minimal or no effects on non-target tissues. The use of a tumorantigen in a vaccine that generates humoral and/or cell-mediated immuneresponses as anti-cancer therapy is well known in the art and has beenemployed in prostate cancer using human PSMA and rodent PAP immunogens(Hodge et al., 1995, Int. J. Cancer 63:231-237; Fong et al., 1997, J.Immunol. 159:3113-3117).

Such methods can be readily practiced by employing a 238P1B2-relatedprotein, or an 238P1B2-encoding nucleic acid molecule and recombinantvectors capable of expressing and presenting the 238P1B2 immunogen(which typically comprises a number of antibody or T cell epitopes).Skilled artisans understand that a wide variety of vaccine systems fordelivery of immunoreactive epitopes are known in the art (see, e.g.,Heryln et al., Ann Med 1999 February 31(1):66-78; Maruyama et al.,Cancer Immunol Immunother 2000 June 49(3):123-32) Briefly, such methodsof generating an immune response (e.g. humoral and/or cell-mediated) ina mammal, comprise the steps of: exposing the mammal's immune system toan immunoreactive epitope (e.g. an epitope present in a 238P1B2 proteinshown in FIG. 3 or analog or homolog thereof) so that the mammalgenerates an immune response that is specific for that epitope (e.g.generates antibodies that specifically recognize that epitope). In apreferred method, a 238P1B2 immunogen contains a biological motif, seee.g., Tables V-XVIII, Table XIX, or a peptide of a size range from238P1B2 indicated in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9.

The entire 238P1B2 protein, immunogenic regions or epitopes thereof canbe combined and delivered by various means. Such vaccine compositionscan include, for example, lipopeptides (e.g., Vitiello, A. et al., J.Clin. Invest. 95:341, 1995), peptide compositions encapsulated inpoly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge,et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptidecompositions contained in immune stimulating complexes (ISCOMS) (see,e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin ExpImmunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs)(see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988;Tam, J. P., J. Immunol. Methods 196:17-32, 1996), peptides formulated asmultivalent peptides; peptides for use in ballistic delivery systems,typically crystallized peptides, viral delivery vectors (Perkus, M. E.et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p.379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. etal., Nature 320:537, 1986; Kieny, M.-P. et al, AIDS Bio/Technology4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda,P. K. et al., Virology 175:535, 1990), particles of viral or syntheticorigin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996;Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. etal., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R.,and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al.,Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol.148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked orparticle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993;Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993;Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S.H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev.Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16,1993). Toxin-targeted delivery technologies, also known as receptormediated targeting, such as those of Avant Immunotherapeutics, Inc.(Needham, Mass.) may also be used.

In patients with 238P1B2-associated cancer, the vaccine compositions ofthe invention can also be used in conjunction with other treatments usedfor cancer, e.g., surgery, chemotherapy, drug therapies, radiationtherapies, etc. including use in combination with immune adjuvants suchas IL-2, IL-12, GM-CSF, and the like.

Cellular Vaccines:

CTL epitopes can be determined using specific algorithms to identifypeptides within 238P1B2 protein that bind corresponding HLA alleles (seee.g., Table IV; Epimer™ and Epimatrix™, Brown University; and, BIMAS,and SYFPEITHI). In a preferred embodiment, a 238P1B2 immunogen containsone or more amino acid sequences identified using techniques well knownin the art, such as the sequences shown in Tables V-XVIII, Table XIX, ora peptide of 8, 9, 10 or 11 amino acids specified by an HLA Class Imotif/supermotif (e.g., Table IV (A), Table IV (D), or Table IV (E))and/or a peptide of at least 9 amino acids that comprises an HLA ClassII motif/supermotif (e.g., Table IV (B) or Table IV (C)). As isappreciated in the art, the HLA Class I binding groove is essentiallyclosed ended so that peptides of only a particular size range can fitinto the groove and be bound, generally HLA Class I epitopes are 8, 9,10, or 11 amino acids long. In contrast, the HLA Class II binding grooveis essentially open ended; therefore a peptide of about 9 or more aminoacids can be bound by an HLA Class II molecule. Due to the bindinggroove differences between HLA Class I and II, HLA Class I motifs arelength specific, i.e., position two of a Class I motif is the secondamino acid in an amino to carboxyl direction of the peptide. The aminoacid positions in a Class II motif are relative only to each other, notthe overall peptide, i.e., additional amino acids can be attached to theamino and/or carboxyl termini of a motif-bearing sequence. HLA Class IIepitopes are often 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, or 25 amino acids long, or longer than 25 amino acids.

Antibody-Based Vaccines

A wide variety of methods for generating an immune response in a mammalare known in the art (for example as the first step in the generation ofhybridomas). Methods of generating an immune response in a mammalcomprise exposing the mammal's immune system to an immunogenic epitopeon a protein (e.g. a 238P1B2 protein) so that an immune response isgenerated. A typical embodiment consists of a method for generating animmune response to 238P1B2 in a host, by contacting the host with asufficient amount of at least one 238P1B2 B cell or cytotoxic T-cellepitope or analog thereof; and at least one periodic interval thereafterre-contacting the host with the 238P1B2 B cell or cytotoxic T-cellepitope or analog thereof. A specific embodiment consists of a method ofgenerating an immune response against a 238P1B2-related protein or aman-made multiepitopic peptide comprising: administering 238P1B2immunogen (e.g. a 238P1B2 protein or a peptide fragment thereof, an238P1B2 fusion protein or analog etc.) in a vaccine preparation to ahuman or another mammal. Typically, such vaccine preparations furthercontain a suitable adjuvant (see, e.g., U.S. Pat. No. 6,146,635) or auniversal helper epitope such as a PADRE™ peptide (Epimmune Inc., SanDiego, Calif.; see, e.g., Alexander et al., J. Immunol. 2000 164(3);164(3): 1625-1633; Alexander et al., Immunity 1994 1(9): 751-761 andAlexander et al., Immunol. Res. 1998 18(2): 79-92). An alternativemethod comprises generating an immune response in an individual againsta 238P1B2 immunogen by: administering in vivo to muscle or skin of theindividual's body a DNA molecule that comprises a DNA sequence thatencodes an 238P1B2 immunogen, the DNA sequence operatively linked toregulatory sequences which control the expression of the DNA sequence;wherein the DNA molecule is taken up by cells, the DNA sequence isexpressed in the cells and an immune response is generated against theimmunogen (see, e.g., U.S. Pat. No. 5,962,428). Optionally a geneticvaccine facilitator such as anionic lipids; saponins; lectins;estrogenic compounds; hydroxylated lower alkyls; dimethyl sulfoxide; andurea is also administered. In addition, an antiidiotypic antibody can beadministered that mimics 238P1B2, in order to generate a response to thetarget antigen.

Nucleic Acid Vaccines:

Vaccine compositions of the invention include nucleic acid-mediatedmodalities. DNA or RNA that encode protein(s) of the invention can beadministered to a patient. Genetic immunization methods can be employedto generate prophylactic or therapeutic humoral and cellular immuneresponses directed against cancer cells expressing 238P1B2. Constructscomprising DNA encoding a 238P1B2-related protein/immunogen andappropriate regulatory sequences can be injected directly into muscle orskin of an individual, such that the cells of the muscle or skin take-upthe construct and express the encoded 238P1B2 protein/immunogen.Alternatively, a vaccine comprises a 238P1B2-related protein. Expressionof the 238P1B2-related protein immunogen results in the generation ofprophylactic or therapeutic humoral and cellular immunity against cellsthat bear a 238P1B2 protein. Various prophylactic and therapeuticgenetic immunization techniques known in the art can be used (forreview, see information and references published at the world wide webInternet address genweb.com). Nucleic acid-based delivery is described,for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S.Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524;5,679,647; WO 98/04720. Examples of DNA-based delivery technologiesinclude “naked DNA”, facilitated (bupivicaine, polymers,peptide-mediated) delivery, cationic lipid complexes, andparticle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g.,U.S. Pat. No. 5,922,687).

For therapeutic or prophylactic immunization purposes, proteins of theinvention can be expressed via viral or bacterial vectors. Various viralgene delivery systems that can be used in the practice of the inventioninclude, but are not limited to, vaccinia, fowlpox, canarypox,adenovirus, influenza, poliovirus, adeno-associated virus, lentivirus,and sindbis virus (see, e.g., Restifo, 1996, Curr. Opin. Immunol.8:658-663; Tsang et al. J. Natl. Cancer Inst. 87:982-990 (1995)).Non-viral delivery systems can also be employed by introducing naked DNAencoding a 238P1B2-related protein into the patient (e.g.,intramuscularly or intradermally) to induce an anti-tumor response.

Vaccinia virus is used, for example, as a vector to express nucleotidesequences that encode the peptides of the invention. Upon introductioninto a host, the recombinant vaccinia virus expresses the proteinimmunogenic peptide, and thereby elicits a host immune response.Vaccinia vectors and methods useful in immunization protocols aredescribed in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG(Bacille Calmette Guerin). BCG vectors are described in Stover et al.,Nature 351:456-460 (1991). A wide variety of other vectors useful fortherapeutic administration or immunization of the peptides of theinvention, e.g. adeno and adeno-associated virus vectors, retroviralvectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, andthe like, will be apparent to those skilled in the art from thedescription herein.

Thus, gene delivery systems are used to deliver a 238P1B2-relatednucleic acid molecule. In one embodiment, the full-length human 238P1B2cDNA is employed. In another embodiment, 238P1B2 nucleic acid moleculesencoding specific cytotoxic T lymphocyte (CTL) and/or antibody epitopesare employed.

Ex Vivo Vaccines

Various ex vivo strategies can also be employed to generate an immuneresponse. One approach involves the use of antigen presenting cells(APCs) such as dendritic cells (DC) to present 238P1B2 antigen to apatient's immune system. Dendritic cells express MHC class I and IImolecules, B7 co-stimulator, and IL-12, and are thus highly specializedantigen presenting cells. In prostate cancer, autologous dendritic cellspulsed with peptides of the prostate-specific membrane antigen (PSMA)are being used in a Phase I clinical trial to stimulate prostate cancerpatients' immune systems (Tjoa et al., 1996, Prostate 28:65-69; Murphyet al., 1996, Prostate 29:371-380). Thus, dendritic cells can be used topresent 238P1B2 peptides to T cells in the context of MHC class I or IImolecules. In one embodiment, autologous dendritic cells are pulsed with238P1B2 peptides capable of binding to MHC class I and/or class IImolecules. In another embodiment, dendritic cells are pulsed with thecomplete 238P1B2 protein. Yet another embodiment involves engineeringthe overexpression of a 238P1B2 gene in dendritic cells using variousimplementing vectors known in the art, such as adenovirus (Arthur etal., 1997, Cancer Gene Ther. 4:17-25), retrovirus (Henderson et al.,1996, Cancer Res. 56:3763-3770), lentivirus, adeno-associated virus, DNAtransfection (Ribas et al., 1997, Cancer Res. 57:2865-2869), ortumor-derived RNA transfection (Ashley et al., 1997, J. Exp. Med.186:1177-1182). Cells that express 238P1B2 can also be engineered toexpress immune modulators, such as GM-CSF, and used as immunizingagents.

X.B.) 238P1B2 as a Target for Antibody-Based Therapy

238P1B2 is an attractive target for antibody-based therapeuticstrategies. A number of antibody strategies are known in the art fortargeting both extracellular and intracellular molecules (see, e.g.,complement and ADCC mediated killing as well as the use of intrabodies).Because 238P1B2 is expressed by cancer cells of various lineagesrelative to corresponding normal cells, systemic administration of238P1B2-immunoreactive compositions are prepared that exhibit excellentsensitivity without toxic, non-specific and/or non-target effects causedby binding of the immunoreactive composition to non-target organs andtissues. Antibodies specifically reactive with domains of 238P1B2 areuseful to treat 238P1B2-expressing cancers systemically, either asconjugates with a toxin or therapeutic agent, or as naked antibodiescapable of inhibiting cell proliferation or function.

238P1B2 antibodies can be introduced into a patient such that theantibody binds to 238P1B2 and modulates a function, such as aninteraction with a binding partner, and consequently mediatesdestruction of the tumor cells and/or inhibits the growth of the tumorcells. Mechanisms by which such antibodies exert a therapeutic effectcan include complement-mediated cytolysis, antibody-dependent cellularcytotoxicity, modulation of the physiological function of 238P1B2,inhibition of ligand binding or signal transduction pathways, modulationof tumor cell differentiation, alteration of tumor angiogenesis factorprofiles, and/or apoptosis.

Those skilled in the art understand that antibodies can be used tospecifically target and bind immunogenic molecules such as animmunogenic region of a 238P1B2 sequence shown in FIG. 2 or FIG. 3. Inaddition, skilled artisans understand that it is routine to conjugateantibodies to cytotoxic agents (see, e.g., Slevers et al. Blood 93:113678-3684 (Jun. 1, 1999)). When cytotoxic and/or therapeutic agents aredelivered directly to cells, such as by conjugating them to antibodiesspecific for a molecule expressed by that cell (e.g. 238P1B2), thecytotoxic agent will exert its known biological effect (i.e.cytotoxicity) on those cells.

A wide variety of compositions and methods for using antibody-cytotoxicagent conjugates to kill cells are known in the art. In the context ofcancers, typical methods entail administering to an animal having atumor a biologically effective amount of a conjugate comprising aselected cytotoxic and/or therapeutic agent linked to a targeting agent(e.g. an anti-238P1B2 antibody) that binds to a marker (e.g. 238P1B2)expressed, accessible to binding or localized on the cell surfaces. Atypical embodiment is a method of delivering a cytotoxic and/ortherapeutic agent to a cell expressing 238P1B2, comprising conjugatingthe cytotoxic agent to an antibody that immunospecifically binds to a238P1B2 epitope, and, exposing the cell to the antibody-agent conjugate.Another illustrative embodiment is a method of treating an individualsuspected of suffering from metastasized cancer, comprising a step ofadministering parenterally to said individual a pharmaceuticalcomposition comprising a therapeutically effective amount of an antibodyconjugated to a cytotoxic and/or therapeutic agent.

Cancer immunotherapy using anti-238P1B2 antibodies can be done inaccordance with various approaches that have been successfully employedin the treatment of other types of cancer, including but not limited tocolon cancer (Arlen et al., 1998, Crit. Rev. Immunol. 18:133-138),multiple myeloma (Ozaki et al., 1997, Blood 90:3179-3186, Tsunenari etal., 1997, Blood 90:2437-2444), gastric cancer (Kasprzyk et al., 1992,Cancer Res. 52:2771-2776), B-cell lymphoma (Funakoshi et al., 1996, J.Immunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhong et al.,1996, Leuk. Res. 20:581-589), colorectal cancer (Moun et al., 1994,Cancer Res. 54:6160-6166; Velders et al., 1995, Cancer Res.55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin.Immunol. 11:117-127). Some therapeutic approaches involve conjugation ofnaked antibody to a toxin or radioisotope, such as the conjugation ofY⁹¹ or I¹³¹ to anti-CD20 antibodies (e.g., Zevalin™, IDECPharmaceuticals Corp. or Bexxar™, Coulter Pharmaceuticals), while othersinvolve co-administration of antibodies and other therapeutic agents,such as Herceptin™ (trastuzumab) with paclitaxel (Genentech, Inc.). Theantibodies can be conjugated to a therapeutic agent. To treat prostatecancer, for example, 238P1B2 antibodies can be administered inconjunction with radiation, chemotherapy or hormone ablation. Also,antibodies can be conjugated to a toxin such as calicheamicin (e.g.,Mylotarg™, Wyeth-Ayerst, Madison, N.J., a recombinant humanized IgG₄kappa antibody conjugated to antitumor antibiotic calicheamicin) or amaytansinoid (e.g., taxane-based Tumor-Activated Prodrug, TAP, platform,ImmunoGen, Cambridge, Mass., also see e.g., U.S. Pat. No. 5,416,064).

Although 238P1B2 antibody therapy is useful for all stages of cancer,antibody therapy can be particularly appropriate in advanced ormetastatic cancers. Treatment with the antibody therapy of the inventionis indicated for patients who have received one or more rounds ofchemotherapy. Alternatively, antibody therapy of the invention iscombined with a chemotherapeutic or radiation regimen for patients whohave not received chemotherapeutic treatment. Additionally, antibodytherapy can enable the use of reduced dosages of concomitantchemotherapy, particularly for patients who do not tolerate the toxicityof the chemotherapeutic agent very well. Fan et al. (Cancer Res.53:4637-4642, 1993), Prewett et al. (International J. of Onco.9:217-224, 1996), and Hancock et al. (Cancer Res. 51:4575-4580, 1991)describe the use of various antibodies together with chemotherapeuticagents.

Although 238P1B2 antibody therapy is useful for all stages of cancer,antibody therapy can be particularly appropriate in advanced ormetastatic cancers. Treatment with the antibody therapy of the inventionis indicated for patients who have received one or more rounds ofchemotherapy. Alternatively, antibody therapy of the invention iscombined with a chemotherapeutic or radiation regimen for patients whohave not received chemotherapeutic treatment. Additionally, antibodytherapy can enable the use of reduced dosages of concomitantchemotherapy, particularly for patients who do not tolerate the toxicityof the chemotherapeutic agent very well.

Cancer patients can be evaluated for the presence and level of 238P1B2expression, preferably using immunohistochemical assessments of tumortissue, quantitative 238P1B2 imaging, or other techniques that reliablyindicate the presence and degree of 238P1B2 expression.Immunohistochemical analysis of tumor biopsies or surgical specimens ispreferred for this purpose. Methods for immunohistochemical analysis oftumor tissues are well known in the art.

Anti-238P1B2 monoclonal antibodies that treat prostate and other cancersinclude those that initiate a potent immune response against the tumoror those that are directly cytotoxic. In this regard, anti-238P1B2monoclonal antibodies (mAbs) can elicit tumor cell lysis by eithercomplement-mediated or antibody-dependent cell cytotoxicity (ADCC)mechanisms, both of which require an intact Fc portion of theimmunoglobulin molecule for interaction with effector cell Fc receptorsites on complement proteins. In addition, anti-238P1B2 mAbs that exerta direct biological effect on tumor growth are useful to treat cancersthat express 238P1B2. Mechanisms by which directly cytotoxic mAbs actinclude: inhibition of cell growth, modulation of cellulardifferentiation, modulation of tumor angiogenesis factor profiles, andthe induction of apoptosis. The mechanism(s) by which a particularanti-238P1B2 mAb exerts an anti-tumor effect is evaluated using anynumber of in vitro assays that evaluate cell death such as ADCC, ADMMC,complement-mediated cell lysis, and so forth, as is generally known inthe art.

In some patients, the use of murine or other non-human monoclonalantibodies, or human/mouse chimeric mAbs can induce moderate to strongimmune responses against the non-human antibody. This can result inclearance of the antibody from circulation and reduced efficacy. In themost severe cases, such an immune response can lead to the extensiveformation of immune complexes which, potentially, can cause renalfailure. Accordingly, preferred monoclonal antibodies used in thetherapeutic methods of the invention are those that are either fullyhuman or humanized and that bind specifically to the target 238P1B2antigen with high affinity but exhibit low or no antigenicity in thepatient.

Therapeutic methods of the invention contemplate the administration ofsingle anti-238P1B2 mAbs as well as combinations, or cocktails, ofdifferent mAbs. Such mAb cocktails can have certain advantages inasmuchas they contain mAbs that target different epitopes, exploit differenteffector mechanisms or combine directly cytotoxic mAbs with mAbs thatrely on immune effector functionality. Such mAbs in combination canexhibit synergistic therapeutic effects. In addition, anti-238P1B2 mAbscan be administered concomitantly with other therapeutic modalities,including but not limited to various chemotherapeutic agents,androgen-blockers, immune modulators (e.g., IL-2, GM-CSF), surgery orradiation. The anti-238P1B2 mAbs are administered in their “naked” orunconjugated form, or can have a therapeutic agent(s) conjugated tothem.

Anti-238P1B2 antibody formulations are administered via any routecapable of delivering the antibodies to a tumor cell. Routes ofadministration include, but are not limited to, intravenous,intraperitoneal, intramuscular, intratumor, intradermal, and the like.Treatment generally involves repeated administration of the anti-238P1B2antibody preparation, via an acceptable route of administration such asintravenous injection (IV), typically at a dose in the range of about0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 15, 20, or 25 mg/kg body weight. In general, doses in the range of10-1000 mg mAb per week are effective and well tolerated.

Based on clinical experience with the Herceptin™ mAb in the treatment ofmetastatic breast cancer, an initial loading dose of approximately 4mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kgIV of the anti-238P1B2 mAb preparation represents an acceptable dosingregimen. Preferably, the initial loading dose is administered as a 90minute or longer infusion. The periodic maintenance dose is administeredas a 30 minute or longer infusion, provided the initial dose was welltolerated. As appreciated by those of skill in the art, various factorscan influence the ideal dose regimen in a particular case. Such factorsinclude, for example, the binding affinity and half life of the Ab ormAbs used, the degree of 238P1B2 expression in the patient, the extentof circulating shed 238P1B2 antigen, the desired steady-state antibodyconcentration level, frequency of treatment, and the influence ofchemotherapeutic or other agents used in combination with the treatmentmethod of the invention, as well as the health status of a particularpatient.

Optionally, patients should be evaluated for the levels of 238P1B2 in agiven sample (e.g. the levels of circulating 238P1B2 antigen and/or238P1B2 expressing cells) in order to assist in the determination of themost effective dosing regimen, etc. Such evaluations are also used formonitoring purposes throughout therapy, and are useful to gaugetherapeutic success in combination with the evaluation of otherparameters (for example, urine cytology and/or ImmunoCyt levels inbladder cancer therapy, or by analogy, serum PSA levels in prostatecancer therapy).

Anti-idiotypic anti-238P1B2 antibodies can also be used in anti-cancertherapy as a vaccine for inducing an immune response to cells expressinga 238P1B2-related protein. In particular, the generation ofanti-idiotypic antibodies is well known in the art; this methodology canreadily be adapted to generate anti-idiotypic anti-238P1B2 antibodiesthat mimic an epitope on a 238P1B2-related protein (see, for example,Wagner et al., 1997, Hybridoma 16: 33-40; Foon et al., 1995, J. Clin.Invest. 96:334-342; Herlyn et al., 1996, Cancer Immunol. Immunother.43:65-76). Such an anti-idiotypic antibody can be used in cancer vaccinestrategies.

X.C.) 238P1B2 as a Target for Cellular Immune Responses

Vaccines and methods of preparing vaccines that contain animmunogenically effective amount of one or more HLA-binding peptides asdescribed herein are further embodiments of the invention. Furthermore,vaccines in accordance with the invention encompass compositions of oneor more of the claimed peptides. A peptide can be present in a vaccineindividually. Alternatively, the peptide can exist as a homopolymercomprising multiple copies of the same peptide, or as a heteropolymer ofvarious peptides. Polymers have the advantage of increased immunologicalreaction and, where different peptide epitopes are used to make up thepolymer, the additional ability to induce antibodies and/or CTLs thatreact with different antigenic determinants of the pathogenic organismor tumor-related peptide targeted for an immune response. Thecomposition can be a naturally occurring region of an antigen or can beprepared, e.g., recombinantly or by chemical synthesis.

Carriers that can be used with vaccines of the invention are well knownin the art, and include, e.g., thyroglobulin, albumins such as humanserum albumin, tetanus toxoid, polyamino acids such as poly L-lysine,poly L-glutamic acid, influenza, hepatitis B virus core protein, and thelike. The vaccines can contain a physiologically tolerable (i.e.,acceptable) diluent such as water, or saline, preferably phosphatebuffered saline. The vaccines also typically include an adjuvant.Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate,aluminum hydroxide, or alum are examples of materials well known in theart. Additionally, as disclosed herein, CTL responses can be primed byconjugating peptides of the invention to lipids, such astripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS). Moreover, anadjuvant such as a syntheticcytosine-phosphorothiolated-guanine-containing (CpG) oligonucleotideshas been found to increase CTL responses 10- to 100-fold. (see, e.g.Davila and Celis J. Immunol. 165:539-547 (2000))

Upon immunization with a peptide composition in accordance with theinvention, via injection, aerosol, oral, transdermal, transmucosal,intrapleural, intrathecal, or other suitable routes, the immune systemof the host responds to the vaccine by producing large amounts of CTLsand/or HTLs specific for the desired antigen. Consequently, the hostbecomes at least partially immune to later development of cells thatexpress or overexpress 238P1B2 antigen, or derives at least sometherapeutic benefit when the antigen was tumor-associated.

In some embodiments, it may be desirable to combine the class I peptidecomponents with components that induce or facilitate neutralizingantibody and or helper T cell responses directed to the target antigen.A preferred embodiment of such a composition comprises class I and classII epitopes in accordance with the invention. An alternative embodimentof such a composition comprises a class I and/or class II epitope inaccordance with the invention, along with a cross reactive HTL epitopesuch as PADRE™ (Epimmune, San Diego, Calif.) molecule (described e.g.,in U.S. Pat. No. 5,736,142).

A vaccine of the invention can also include antigen-presenting cells(APC), such as dendritic cells (DC), as a vehicle to present peptides ofthe invention. Vaccine compositions can be created in vitro, followingdendritic cell mobilization and harvesting, whereby loading of dendriticcells occurs in vitro. For example, dendritic cells are transfected,e.g., with a minigene in accordance with the invention, or are pulsedwith peptides. The dendritic cell can then be administered to a patientto elicit immune responses in vivo. Vaccine compositions, either DNA- orpeptide-based, can also be administered in vivo in combination withdendritic cell mobilization whereby loading of dendritic cells occurs invivo.

Preferably, the following principles are utilized when selecting anarray of epitopes for inclusion in a polyepitopic composition for use ina vaccine, or for selecting discrete epitopes to be included in avaccine and/or to be encoded by nucleic acids such as a minigene. It ispreferred that each of the following principles be balanced in order tomake the selection. The multiple epitopes to be incorporated in a givenvaccine composition may be, but need not be, contiguous in sequence inthe native antigen from which the epitopes are derived.

1.) Epitopes are selected which, upon administration, mimic immuneresponses that have been observed to be correlated with tumor clearance.For HLA Class I this includes 3-4 epitopes that come from at least onetumor associated antigen (TAA). For HLA Class II a similar rationale isemployed; again 3-4 epitopes are selected from at least one TAA (see,e.g., Rosenberg et al., Science 278:1447-1450). Epitopes from one TAAmay be used in combination with epitopes from one or more additionalTAAs to produce a vaccine that targets tumors with varying expressionpatterns of frequently-expressed TAAs.

2.) Epitopes are selected that have the requisite binding affinityestablished to be correlated with immunogenicity: for HLA Class I anIC₅₀ of 500 nM or less, often 200 nM or less; and for Class II an IC₅₀of 1000 nM or less.

3.) Sufficient supermotif bearing-peptides, or a sufficient array ofallele-specific motif-bearing peptides, are selected to give broadpopulation coverage. For example, it is preferable to have at least 80%population coverage. A Monte Carlo analysis, a statistical evaluationknown in the art, can be employed to assess the breadth, or redundancyof, population coverage.

4.) When selecting epitopes from cancer-related antigens it is oftenuseful to select analogs because the patient may have developedtolerance to the native epitope.

5.) Of particular relevance are epitopes referred to as “nestedepitopes.” Nested epitopes occur where at least two epitopes overlap ina given peptide sequence. A nested peptide sequence can comprise B cell,HLA class I and/or HLA class II epitopes. When providing nestedepitopes, a general objective is to provide the greatest number ofepitopes per sequence. Thus, an aspect is to avoid providing a peptidethat is any longer than the amino terminus of the amino terminal epitopeand the carboxyl terminus of the carboxyl terminal epitope in thepeptide. When providing a multi-epitopic sequence, such as a sequencecomprising nested epitopes, it is generally important to screen thesequence in order to insure that it does not have pathological or otherdeleterious biological properties.

6.) If a polyepitopic protein is created, or when creating a minigene,an objective is to generate the smallest peptide that encompasses theepitopes of interest. This principle is similar, if not the same as thatemployed when selecting a peptide comprising nested epitopes. However,with an artificial polyepitopic peptide, the size minimization objectiveis balanced against the need to integrate any spacer sequences betweenepitopes in the polyepitopic protein. Spacer amino acid residues can,for example, be introduced to avoid junctional epitopes (an epitoperecognized by the immune system, not present in the target antigen, andonly created by the man-made juxtaposition of epitopes), or tofacilitate cleavage between epitopes and thereby enhance epitopepresentation. Junctional epitopes are generally to be avoided becausethe recipient may generate an immune response to that non-nativeepitope. Of particular concern is a junctional epitope that is a“dominant epitope.” A dominant epitope may lead to such a zealousresponse that immune responses to other epitopes are diminished orsuppressed.

7.) Where the sequences of multiple variants of the same target proteinare present, potential peptide epitopes can also be selected on thebasis of their conservancy. For example, a criterion for conservancy maydefine that the entire sequence of an HLA class I binding peptide or theentire 9-mer core of a class II binding peptide be conserved in adesignated percentage of the sequences evaluated for a specific proteinantigen.

X.C.1. Minigene Vaccines

A number of different approaches are available which allow simultaneousdelivery of multiple epitopes. Nucleic acids encoding the peptides ofthe invention are a particularly useful embodiment of the invention.Epitopes for inclusion in a minigene are preferably selected accordingto the guidelines set forth in the previous section. A preferred meansof administering nucleic acids encoding the peptides of the inventionuses minigene constructs encoding a peptide comprising one or multipleepitopes of the invention.

The use of multi-epitope minigenes is described below and in, Ishioka etal., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J.Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996;Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine16:426, 1998. For example, a multi-epitope DNA plasmid encodingsupermotif- and/or motif-bearing epitopes derived 238P1B2, the PADRE®universal helper T cell epitope (or multiple HTL epitopes from 238P1B2),and an endoplasmic reticulum-translocating signal sequence can beengineered. A vaccine may also comprise epitopes that are derived fromother TAAs.

The immunogenicity of a multi-epitopic minigene can be confirmed intransgenic mice to evaluate the magnitude of CTL induction responsesagainst the epitopes tested. Further, the immunogenicity of DNA-encodedepitopes in vivo can be correlated with the in vitro responses ofspecific CTL lines against target cells transfected with the DNAplasmid. Thus, these experiments can show that the minigene serves toboth: 1.) generate a CTL response and 2.) that the induced CTLsrecognized cells expressing the encoded epitopes.

For example, to create a DNA sequence encoding the selected epitopes(minigene) for expression in human cells, the amino acid sequences ofthe epitopes may be reverse translated. A human codon usage table can beused to guide the codon choice for each amino acid. Theseepitope-encoding DNA sequences may be directly adjoined, so that whentranslated, a continuous polypeptide sequence is created. To optimizeexpression and/or immunogenicity, additional elements can beincorporated into the minigene design. Examples of amino acid sequencesthat can be reverse translated and included in the minigene sequenceinclude: HLA class I epitopes, HLA class II epitopes, antibody epitopes,a ubiquitination signal sequence, and/or an endoplasmic reticulumtargeting signal. In addition, HLA presentation of CTL and HTL epitopesmay be improved by including synthetic (e.g. poly-alanine) ornaturally-occurring flanking sequences adjacent to the CTL or HTLepitopes; these larger peptides comprising the epitope(s) are within thescope of the invention.

The minigene sequence may be converted to DNA by assemblingoligonucleotides that encode the plus and minus strands of the minigene.Overlapping oligonucleotides (30-100 bases long) may be synthesized,phosphorylated, purified and annealed under appropriate conditions usingwell known techniques. The ends of the oligonucleotides can be joined,for example, using T4 DNA ligase. This synthetic minigene, encoding theepitope polypeptide, can then be cloned into a desired expressionvector.

Standard regulatory sequences well known to those of skill in the artare preferably included in the vector to ensure expression in the targetcells. Several vector elements are desirable: a promoter with adown-stream cloning site for minigene insertion; a polyadenylationsignal for efficient transcription termination; an E. coli origin ofreplication; and an E. coli selectable marker (e.g. ampicillin orkanamycin resistance). Numerous promoters can be used for this purpose,e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat.Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Additional vector modifications may be desired to optimize minigeneexpression and immunogenicity. In some cases, introns are required forefficient gene expression, and one or more synthetic ornaturally-occurring introns could be incorporated into the transcribedregion of the minigene. The inclusion of mRNA stabilization sequencesand sequences for replication in mammalian cells may also be consideredfor increasing minigene expression.

Once an expression vector is selected, the minigene is cloned into thepolylinker region downstream of the promoter. This plasmid istransformed into an appropriate E. coli strain, and DNA is preparedusing standard techniques. The orientation and DNA sequence of theminigene, as well as all other elements included in the vector, areconfirmed using restriction mapping and DNA sequence analysis. Bacterialcells harboring the correct plasmid can be stored as a master cell bankand a working cell bank.

In addition, immunostimulatory sequences (ISSs or CpGs) appear to play arole in the immunogenicity of DNA vaccines. These sequences may beincluded in the vector, outside the minigene coding sequence, if desiredto enhance immunogenicity.

In some embodiments, a bi-cistronic expression vector which allowsproduction of both the minigene-encoded epitopes and a second protein(included to enhance or decrease immunogenicity) can be used. Examplesof proteins or polypeptides that could beneficially enhance the immuneresponse if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF),cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, orfor HTL responses, pan-DR binding proteins (PADRE™, Epimmune, San Diego,Calif.). Helper (HTL) epitopes can be joined to intracellular targetingsignals and expressed separately from expressed CTL epitopes; thisallows direction of the HTL epitopes to a cell compartment differentthan that of the CTL epitopes. If required, this could facilitate moreefficient entry of HTL epitopes into the HLA class II pathway, therebyimproving HTL induction. In contrast to HTL or CTL induction,specifically decreasing the immune response by co-expression ofimmunosuppressive molecules (e.g. TGF-β) may be beneficial in certaindiseases.

Therapeutic quantities of plasmid DNA can be produced for example, byfermentation in E. coli, followed by purification. Aliquots from theworking cell bank are used to inoculate growth medium, and grown tosaturation in shaker flasks or a bioreactor according to well-knowntechniques. Plasmid DNA can be purified using standard bioseparationtechnologies such as solid phase anion-exchange resins supplied byQIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can beisolated from the open circular and linear forms using gelelectrophoresis or other methods.

Purified plasmid DNA can be prepared for injection using a variety offormulations. The simplest of these is reconstitution of lyophilized DNAin sterile phosphate-buffer saline (PBS). This approach, known as “nakedDNA,” is currently being used for intramuscular (IM) administration inclinical trials. To maximize the immunotherapeutic effects of minigeneDNA vaccines, an alternative method for formulating purified plasmid DNAmay be desirable. A variety of methods have been described, and newtechniques may become available. Cationic lipids, glycolipids, andfusogenic liposomes can also be used in the formulation (see, e.g., asdescribed by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7):682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al.,Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In addition, peptides andcompounds referred to collectively as protective, interactive,non-condensing compounds (PINC) could also be complexed to purifiedplasmid DNA to influence variables such as stability, intramusculardispersion, or trafficking to specific organs or cell types.

Target cell sensitization can be used as a functional assay forexpression and HLA class I presentation of minigene-encoded CTLepitopes. For example, the plasmid DNA is introduced into a mammaliancell line that is suitable as a target for standard CTL chromium releaseassays. The transfection method used will be dependent on the finalformulation. Electroporation can be used for “naked” DNA, whereascationic lipids allow direct in vitro transfection. A plasmid expressinggreen fluorescent protein (GFP) can be co-transfected to allowenrichment of transfected cells using fluorescence activated cellsorting (FACS). These cells are then chromium-51 (⁵¹Cr) labeled and usedas target cells for epitope-specific CTL lines; cytolysis, detected by⁵¹Cr release, indicates both production of, and HLA presentation of,minigene-encoded CTL epitopes. Expression of HTL epitopes may beevaluated in an analogous manner using assays to assess HTL activity.

In vivo immunogenicity is a second approach for functional testing ofminigene DNA formulations. Transgenic mice expressing appropriate humanHLA proteins are immunized with the DNA product. The dose and route ofadministration are formulation dependent (e.g., IM for DNA in PBS,intraperitoneal (i.p.) for lipid-complexed DNA). Twenty-one days afterimmunization, splenocytes are harvested and restimulated for one week inthe presence of peptides encoding each epitope being tested. Thereafter,for CTL effector cells, assays are conducted for cytolysis ofpeptide-loaded, ⁵¹Cr-labeled target cells using standard techniques.Lysis of target cells that were sensitized by HLA loaded with peptideepitopes, corresponding to minigene-encoded epitopes, demonstrates DNAvaccine function for in vivo induction of CTLs. Immunogenicity of HTLepitopes is confirmed in transgenic mice in an analogous manner.

Alternatively, the nucleic acids can be administered using ballisticdelivery as described, for instance, in U.S. Pat. No. 5,204,253. Usingthis technique, particles comprised solely of DNA are administered. In afurther alternative embodiment, DNA can be adhered to particles, such asgold particles.

Minigenes can also be delivered using other bacterial or viral deliverysystems well known in the art, e.g., an expression construct encodingepitopes of the invention can be incorporated into a viral vector suchas vaccinia.

X.C.2. Combinations of CTL Peptides with Helper Peptides

Vaccine compositions comprising CTL peptides of the invention can bemodified, e.g., analoged, to provide desired attributes, such asimproved serum half life, broadened population coverage or enhancedimmunogenicity.

For instance, the ability of a peptide to induce CTL activity can beenhanced by linking the peptide to a sequence which contains at leastone epitope that is capable of inducing a T helper cell response.Although a CTL peptide can be directly linked to a T helper peptide,often CTL epitope/HTL epitope conjugates are linked by a spacermolecule. The spacer is typically comprised of relatively small, neutralmolecules, such as amino acids or amino acid mimetics, which aresubstantially uncharged under physiological conditions. The spacers aretypically selected from, e.g., Ala, Gly, or other neutral spacers ofnonpolar amino acids or neutral polar amino acids. It will be understoodthat the optionally present spacer need not be comprised of the sameresidues and thus may be a hetero- or homo-oligomer. When present, thespacer will usually be at least one or two residues, more usually threeto six residues and sometimes 10 or more residues. The CTL peptideepitope can be linked to the T helper peptide epitope either directly orvia a spacer either at the amino or carboxy terminus of the CTL peptide.The amino terminus of either the immunogenic peptide or the T helperpeptide may be acylated.

In certain embodiments, the T helper peptide is one that is recognizedby T helper cells present in a majority of a genetically diversepopulation. This can be accomplished by selecting peptides that bind tomany, most, or all of the HLA class II molecules. Examples of such aminoacid bind many HLA Class II molecules include sequences from antigenssuch as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID: 1),Plasmodium falciparum circumsporozoite (CS) protein at positions 378-398(DIEKKIAKMEKASSVFNVVNS; SEQ ID: 2), and Streptococcus 18 kD protein atpositions 116-131 (GAVDSILGGVATYGAA; SEQ ID: 3). Other examples includepeptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.

Alternatively, it is possible to prepare synthetic peptides capable ofstimulating T helper lymphocytes, in a loosely HLA-restricted fashion,using amino acid sequences not found in nature (see, e.g., PCTpublication WO 95/07707). These synthetic compounds calledPan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego,Calif.) are designed to most preferably bind most HLA-DR (human HLAclass II) molecules. For instance, a pan-DR-binding epitope peptidehaving the formula: aKXVAAWTLKAAa (SEQ ID: 4), where “X” is eithercyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanineor L-alanine, has been found to bind to most HLA-DR alleles, and tostimulate the response of T helper lymphocytes from most individuals,regardless of their HLA type. An alternative of a pan-DR binding epitopecomprises all “L” natural amino acids and can be provided in the form ofnucleic acids that encode the epitope.

HTL peptide epitopes can also be modified to alter their biologicalproperties. For example, they can be modified to include D-amino acidsto increase their resistance to proteases and thus extend their serumhalf life, or they can be conjugated to other molecules such as lipids,proteins, carbohydrates, and the like to increase their biologicalactivity. For example, a T helper peptide can be conjugated to one ormore palmitic acid chains at either the amino or carboxyl termini.

X.C.3. Combinations of CTL Peptides with T Cell Priming Agents

In some embodiments it may be desirable to include in the pharmaceuticalcompositions of the invention at least one component which primes Blymphocytes or T lymphocytes. Lipids have been identified as agentscapable of priming CTL in vivo. For example, palmitic acid residues canbe attached to the ε- and α-amino groups of a lysine residue and thenlinked, e.g., via one or more linking residues such as Gly, Gly-Gly-,Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidatedpeptide can then be administered either directly in a micelle orparticle, incorporated into a liposome, or emulsified in an adjuvant,e.g., incomplete Freund's adjuvant. In a preferred embodiment, aparticularly effective immunogenic composition comprises palmitic acidattached to ε- and α-amino groups of Lys, which is attached via linkage,e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

As another example of lipid priming of CTL responses, E. colilipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine(P₃CSS) can be used to prime virus specific CTL when covalently attachedto an appropriate peptide (see, e.g., Deres, et al., Nature 342:561,1989). Peptides of the invention can be coupled to P₃CSS, for example,and the lipopeptide administered to an individual to specifically primean immune response to the target antigen. Moreover, because theinduction of neutralizing antibodies can also be primed withP₃CSS-conjugated epitopes, two such compositions can be combined to moreeffectively elicit both humoral and cell-mediated responses.

X.C.4. Vaccine Compositions Comprising Dc Pulsed with CTL and/or HTLPeptides

An embodiment of a vaccine composition in accordance with the inventioncomprises ex vivo administration of a cocktail of epitope-bearingpeptides to PBMC, or isolated DC therefrom, from the patient's blood. Apharmaceutical to facilitate harvesting of DC can be used, such asProgenipoietin™ (Pharmacia-Monsanto, St. Louis, Mo.) or GM-CSF/IL-4.After pulsing the DC with peptides and prior to reinfusion intopatients, the DC are washed to remove unbound peptides. In thisembodiment, a vaccine comprises peptide-pulsed DCs which present thepulsed peptide epitopes complexed with HLA molecules on their surfaces.

The DC can be pulsed ex vivo with a cocktail of peptides, some of whichstimulate CTL responses to 238P1B2. Optionally, a helper T cell (HTL)peptide, such as a natural or artificial loosely restricted HLA Class IIpeptide, can be included to facilitate the CTL response. Thus, a vaccinein accordance with the invention is used to treat a cancer whichexpresses or overexpresses 238P1B2.

X.D. Adoptive Immunotherapy

Antigenic 238P1B2-related peptides are used to elicit a CTL and/or HTLresponse ex vivo, as well. The resulting CTL or HTL cells, can be usedto treat tumors in patients that do not respond to other conventionalforms of therapy, or will not respond to a therapeutic vaccine peptideor nucleic acid in accordance with the invention. Ex vivo CTL or HTLresponses to a particular antigen are induced by incubating in tissueculture the patient's, or genetically compatible, CTL or HTL precursorcells together with a source of antigen-presenting cells (APC), such asdendritic cells, and the appropriate immunogenic peptide. After anappropriate incubation time (typically about 7-28 days), in which theprecursor cells are activated and expanded into effector cells, thecells are infused back into the patient, where they will destroy (CTL)or facilitate destruction (HTL) of their specific target cell (e.g., atumor cell). Transfected dendritic cells may also be used as antigenpresenting cells.

X.E. Administration of Vaccines for Therapeutic or Prophylactic Purposes

Pharmaceutical and vaccine compositions of the invention are typicallyused to treat and/or prevent a cancer that expresses or overexpresses238P1B2. In therapeutic applications, peptide and/or nucleic acidcompositions are administered to a patient in an amount sufficient toelicit an effective B cell, CTL and/or HTL response to the antigen andto cure or at least partially arrest or slow symptoms and/orcomplications. An amount adequate to accomplish this is defined as“therapeutically effective dose.” Amounts effective for this use willdepend on, e.g., the particular composition administered, the manner ofadministration, the stage and severity of the disease being treated, theweight and general state of health of the patient, and the judgment ofthe prescribing physician.

For pharmaceutical compositions, the immunogenic peptides of theinvention, or DNA encoding them, are generally administered to anindividual already bearing a tumor that expresses 238P1B2. The peptidesor DNA encoding them can be administered individually or as fusions ofone or more peptide sequences. Patients can be treated with theimmunogenic peptides separately or in conjunction with other treatments,such as surgery, as appropriate.

For therapeutic use, administration should generally begin at the firstdiagnosis of 238P1B2-associated cancer. This is followed by boostingdoses until at least symptoms are substantially abated and for a periodthereafter. The embodiment of the vaccine composition (i.e., including,but not limited to embodiments such as peptide cocktails, polyepitopicpolypeptides, minigenes, or TAA-specific CTLs or pulsed dendritic cells)delivered to the patient may vary according to the stage of the diseaseor the patient's health status. For example, in a patient with a tumorthat expresses 238P1B2, a vaccine comprising 238P1B2-specific CTL may bemore efficacious in killing tumor cells in patient with advanced diseasethan alternative embodiments.

It is generally important to provide an amount of the peptide epitopedelivered by a mode of administration sufficient to effectivelystimulate a cytotoxic T cell response; compositions which stimulatehelper T cell responses can also be given in accordance with thisembodiment of the invention.

The dosage for an initial therapeutic immunization generally occurs in aunit dosage range where the lower value is about 1, 5, 50, 500, or 1,000μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg.Dosage values for a human typically range from about 500 μg to about50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0μg to about 50,000 μg of peptide pursuant to a boosting regimen overweeks to months may be administered depending upon the patient'sresponse and condition as determined by measuring the specific activityof CTL and HTL obtained from the patient's blood. Administration shouldcontinue until at least clinical symptoms or laboratory tests indicatethat the neoplasia, has been eliminated or reduced and for a periodthereafter. The dosages, routes of administration, and dose schedulesare adjusted in accordance with methodologies known in the art.

In certain embodiments, the peptides and compositions of the presentinvention are employed in serious disease states, that is,life-threatening or potentially life threatening situations. In suchcases, as a result of the minimal amounts of extraneous substances andthe relative nontoxic nature of the peptides in preferred compositionsof the invention, it is possible and may be felt desirable by thetreating physician to administer substantial excesses of these peptidecompositions relative to these stated dosage amounts.

The vaccine compositions of the invention can also be used purely asprophylactic agents. Generally the dosage for an initial prophylacticimmunization generally occurs in a unit dosage range where the lowervalue is about 1, 5, 50, 500, or 1000 μg and the higher value is about10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a humantypically range from about 500 μg to about 50,000 μg per 70 kilogrampatient. This is followed by boosting dosages of between about 1.0 μg toabout 50,000 μg of peptide administered at defined intervals from aboutfour weeks to six months after the initial administration of vaccine.The immunogenicity of the vaccine can be assessed by measuring thespecific activity of CTL and HTL obtained from a sample of the patient'sblood.

The pharmaceutical compositions for therapeutic treatment are intendedfor parenteral, topical, oral, nasal, intrathecal, or local (e.g. as acream or topical ointment) administration. Preferably, thepharmaceutical compositions are administered parentally, e.g.,intravenously, subcutaneously, intradermally, or intramuscularly. Thus,the invention provides compositions for parenteral administration whichcomprise a solution of the immunogenic peptides dissolved or suspendedin an acceptable carrier, preferably an aqueous carrier.

A variety of aqueous carriers may be used, e.g., water, buffered water,0.8% saline, 0.3% glycine, hyaluronic acid and the like. Thesecompositions may be sterilized by conventional, well-known sterilizationtechniques, or may be sterile filtered. The resulting aqueous solutionsmay be packaged for use as is, or lyophilized, the lyophilizedpreparation being combined with a sterile solution prior toadministration.

The compositions may contain pharmaceutically acceptable auxiliarysubstances as required to approximate physiological conditions, such aspH-adjusting and buffering agents, tonicity adjusting agents, wettingagents, preservatives, and the like, for example, sodium acetate, sodiumlactate, sodium chloride, potassium chloride, calcium chloride, sorbitanmonolaurate, triethanolamine oleate, etc.

The concentration of peptides of the invention in the pharmaceuticalformulations can vary widely, i.e., from less than about 0.1%, usuallyat or at least about 2% to as much as 20% to 50% or more by weight, andwill be selected primarily by fluid volumes, viscosities, etc., inaccordance with the particular mode of administration selected.

A human unit dose form of a composition is typically included in apharmaceutical composition that comprises a human unit dose of anacceptable carrier, in one embodiment an aqueous carrier, and isadministered in a volume/quantity that is known by those of skill in theart to be used for administration of such compositions to humans (see,e.g., Remington's Pharmaceutical Sciences, 17^(th) Edition, A. Gennaro,Editor, Mack Publishing Co., Easton, Pa., 1985). For example a peptidedose for initial immunization can be from about 1 to about 50,000 μg,generally 100-5,000 μg, for a 70 kg patient. For example, for nucleicacids an initial immunization may be performed using an expressionvector in the form of naked nucleic acid administered IM (or SC or ID)in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to1000 μg) can also be administered using a gene gun. Following anincubation period of 3-4 weeks, a booster dose is then administered. Thebooster can be recombinant fowlpox virus administered at a dose of 5-10⁷to 5×10⁹ pfu.

For antibodies, a treatment generally involves repeated administrationof the anti-238P1B2 antibody preparation, via an acceptable route ofadministration such as intravenous injection (IV), typically at a dosein the range of about 0.1 to about 10 mg/kg body weight. In general,doses in the range of 10-500 mg mAb per week are effective and welltolerated. Moreover, an initial loading dose of approximately 4 mg/kgpatient body weight IV, followed by weekly doses of about 2 mg/kg IV ofthe anti-238P1B2 mAb preparation represents an acceptable dosingregimen. As appreciated by those of skill in the art, various factorscan influence the ideal dose in a particular case. Such factors include,for example, half life of a composition, the binding affinity of an Ab,the immunogenicity of a substance, the degree of 238P1B2 expression inthe patient, the extent of circulating shed 238P1B2 antigen, the desiredsteady-state concentration level, frequency of treatment, and theinfluence of chemotherapeutic or other agents used in combination withthe treatment method of the invention, as well as the health status of aparticular patient. Non-limiting preferred human unit doses are, forexample, 500 μg-1 mg, 1 mg-50 mg, 50 mg-100 mg, 100 mg-200 mg, 200mg-300 mg, 400 mg-500 mg, 500 mg-600 mg, 600 mg-700 mg, 700 mg-800 mg,800 mg-900 mg, 900 mg-1 g, or 1 mg-700 mg. In certain embodiments, thedose is in a range of 2-5 mg/kg body weight, e.g., with follow on weeklydoses of 1-3 mg/kg; 0.5 mg, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 mg/kg bodyweight followed, e.g., in two, three or four weeks by weekly doses;0.5-10 mg/kg body weight, e.g., followed in two, three or four weeks byweekly doses; 225, 250, 275, 300, 325, 350, 375, 400 mg m² of body areaweekly; 1-600 mg m² of body area weekly; 225-400 mg m² of body areaweekly; these does can be followed by weekly doses for 2, 3, 4, 5, 6, 7,8, 9, 19, 11, 12 or more weeks.

In one embodiment, human unit dose forms of polynucleotides comprise asuitable dosage range or effective amount that provides any therapeuticeffect. As appreciated by one of ordinary skill in the art a therapeuticeffect depends on a number of factors, including the sequence of thepolynucleotide, molecular weight of the polynucleotide and route ofadministration. Dosages are generally selected by the physician or otherhealth care professional in accordance with a variety of parametersknown in the art, such as severity of symptoms, history of the patientand the like. Generally, for a polynucleotide of about 20 bases, adosage range may be selected from, for example, an independentlyselected lower limit such as about 0.1, 0.25, 0.5, 1, 2, 5, 10, 20, 30,40, 50, 60, 70, 80, 90, 100, 200, 300, 400 or 500 mg/kg up to anindependently selected upper limit, greater than the lower limit, ofabout 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 3000,4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For example, a dosemay be about any of the following: 0.1 to 100 mg/kg, 0.1 to 50 mg/kg,0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500 mg/kg, 100 to 400 mg/kg, 200to 300 mg/kg, 1 to 100 mg/kg, 100 to 200 mg/kg, 300 to 400 mg/kg, 400 to500 mg/kg, 500 to 1000 mg/kg, 500 to 5000 mg/kg, or 500 to 10,000 mg/kg.Generally, parenteral routes of administration may require higher dosesof polynucleotide compared to more direct application to the nucleotideto diseased tissue, as do polynucleotides of increasing length.

In one embodiment, human unit dose forms of T-cells comprise a suitabledosage range or effective amount that provides any therapeutic effect.As appreciated by one of ordinary skill in the art, a therapeutic effectdepends on a number of factors. Dosages are generally selected by thephysician or other health care professional in accordance with a varietyof parameters known in the art, such as severity of symptoms, history ofthe patient and the like. A dose may be about 10⁴ cells to about 10⁶cells, about 10⁶ cells to about 10⁸ cells, about 10⁸ to about 10¹¹cells, or about 10⁸ to about 5×10¹⁰ cells. A dose may also about 10⁶cells/m² to about 10¹⁰ cells/m², or about 10⁶ cells/m² to about 10⁸cells/m².

Proteins(s) of the invention, and/or nucleic acids encoding theprotein(s), can also be administered via liposomes, which may also serveto: 1) target the proteins(s) to a particular tissue, such as lymphoidtissue; 2) to target selectively to diseases cells; or, 3) to increasethe half-life of the peptide composition. Liposomes include emulsions,foams, micelles, insoluble monolayers, liquid crystals, phospholipiddispersions, lamellar layers and the like. In these preparations, thepeptide to be delivered is incorporated as part of a liposome, alone orin conjunction with a molecule which binds to a receptor prevalent amonglymphoid cells, such as monoclonal antibodies which bind to the CD45antigen, or with other therapeutic or immunogenic compositions. Thus,liposomes either filled or decorated with a desired peptide of theinvention can be directed to the site of lymphoid cells, where theliposomes then deliver the peptide compositions. Liposomes for use inaccordance with the invention are formed from standard vesicle-forminglipids, which generally include neutral and negatively chargedphospholipids and a sterol, such as cholesterol. The selection of lipidsis generally guided by consideration of, e.g., liposome size, acidlability and stability of the liposomes in the blood stream. A varietyof methods are available for preparing liposomes, as described in, e.g.,Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat.Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

For targeting cells of the immune system, a ligand to be incorporatedinto the liposome can include, e.g., antibodies or fragments thereofspecific for cell surface determinants of the desired immune systemcells. A liposome suspension containing a peptide may be administeredintravenously, locally, topically, etc. in a dose which varies accordingto, inter alia, the manner of administration, the peptide beingdelivered, and the stage of the disease being treated.

For solid compositions, conventional nontoxic solid carriers may be usedwhich include, for example, pharmaceutical grades of mannitol, lactose,starch, magnesium stearate, sodium saccharin, talcum, cellulose,glucose, sucrose, magnesium carbonate, and the like. For oraladministration, a pharmaceutically acceptable nontoxic composition isformed by incorporating any of the normally employed excipients, such asthose carriers previously listed, and generally 10-95% of activeingredient, that is, one or more peptides of the invention, and morepreferably at a concentration of 25%-75%.

For aerosol administration, immunogenic peptides are preferably suppliedin finely divided form along with a surfactant and propellant. Typicalpercentages of peptides are about 0.01%-20% by weight, preferably about1%-10%. The surfactant must, of course, be nontoxic, and preferablysoluble in the propellant. Representative of such agents are the estersor partial esters of fatty acids containing from about 6 to 22 carbonatoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic,linolenic, olesteric and oleic acids with an aliphatic polyhydricalcohol or its cyclic anhydride. Mixed esters, such as mixed or naturalglycerides may be employed. The surfactant may constitute about 0.1%-20%by weight of the composition, preferably about 0.25-5%. The balance ofthe composition is ordinarily propellant. A carrier can also beincluded, as desired, as with, e.g., lecithin for intranasal delivery.

XI.) Diagnostic and Prognostic Embodiments of 238P1B2

As disclosed herein, 238P1B2 polynucleotides, polypeptides, reactivecytotoxic T cells (CTL), reactive helper T cells (HTL) andanti-polypeptide antibodies are used in well known diagnostic,prognostic and therapeutic assays that examine conditions associatedwith dysregulated cell growth such as cancer, in particular the cancerslisted in Table I (see, e.g., both its specific pattern of tissueexpression as well as its overexpression in certain cancers as describedfor example in Example 4).

238P1B2 can be analogized to a prostate associated antigen PSA, thearchetypal marker that has been used by medical practitioners for yearsto identify and monitor the presence of prostate cancer (see, e.g.,Merrill et al., J. Urol. 163(2): 503-5120 (2000); Polascik et al., J.Urol. August; 162(2):293-306 (1999) and Fortier et al., J. Nat. CancerInst. 91(19): 1635-1640 (1999)). A variety of other diagnostic markersare also used in similar contexts including p53 and K-ras (see, e.g.,Tulchinsky et al., Int J Mol Med 1999 July 4(1):99-102 and Minimoto etal., Cancer Detect Prev 2000; 24(1):1-12). Therefore, this disclosure of238P1B2 polynucleotides and polypeptides (as well as 238P1B2polynucleotide probes and anti-238P1B2 antibodies used to identify thepresence of these molecules) and their properties allows skilledartisans to utilize these molecules in methods that are analogous tothose used, for example, in a variety of diagnostic assays directed toexamining conditions associated with cancer.

Typical embodiments of diagnostic methods which utilize the 238P1B2polynucleotides, polypeptides, reactive T cells and antibodies areanalogous to those methods from well-established diagnostic assays whichemploy, e.g., PSA polynucleotides, polypeptides, reactive T cells andantibodies. For example, just as PSA polynucleotides are used as probes(for example in Northern analysis, see, e.g., Sharief et al., Biochem.Mol. Biol. Int. 33(3):567-74 (1994)) and primers (for example in PCRanalysis, see, e.g., Okegawa et al., J. Urol. 163(4): 1189-1190 (2000))to observe the presence and/or the level of PSA mRNAs in methods ofmonitoring PSA overexpression or the metastasis of prostate cancers, the238P1B2 polynucleotides described herein can be utilized in the same wayto detect 238P1B2 overexpression or the metastasis of prostate and othercancers expressing this gene. Alternatively, just as PSA polypeptidesare used to generate antibodies specific for PSA which can then be usedto observe the presence and/or the level of PSA proteins in methods tomonitor PSA protein overexpression (see, e.g., Stephan et al., Urology55(4):560-3 (2000)) or the metastasis of prostate cells (see, e.g.,Alanen et al., Pathol. Res. Pract. 192(3):233-7 (1996)), the 238P1B2polypeptides described herein can be utilized to generate antibodies foruse in detecting 238P1B2 overexpression or the metastasis of prostatecells and cells of other cancers expressing this gene.

Specifically, because metastases involves the movement of cancer cellsfrom an organ of origin (such as the lung or prostate gland etc.) to adifferent area of the body (such as a lymph node), assays which examinea biological sample for the presence of cells expressing 238P1B2polynucleotides and/or polypeptides can be used to provide evidence ofmetastasis. For example, when a biological sample from tissue that doesnot normally contain 238P1B2-expressing cells (lymph node) is found tocontain 238P1B2-expressing cells such as the 238P1B2 expression seen inLAPC4 and LAPC9, xenografts isolated from lymph node and bonemetastasis, respectively, this finding is indicative of metastasis.

Alternatively 238P1B2 polynucleotides and/or polypeptides can be used toprovide evidence of cancer, for example, when cells in a biologicalsample that do not normally express 238P1B2 or express 238P1B2 at adifferent level are found to express 238P1B2 or have an increasedexpression of 238P1B2 (see, e.g., the 238P1B2 expression in the cancerslisted in Table I and in patient samples etc. shown in the accompanyingFigures). In such assays, artisans may further wish to generatesupplementary evidence of metastasis by testing the biological samplefor the presence of a second tissue restricted marker (in addition to238P1B2) such as PSA, PSCA etc. (see, e.g., Alanen et al., Pathol. Res.Pract. 192(3): 233-237 (1996)).

Just as PSA polynucleotide fragments and polynucleotide variants areemployed by skilled artisans for use in methods of monitoring PSA,238P1B2 polynucleotide fragments and polynucleotide variants are used inan analogous manner. In particular, typical PSA polynucleotides used inmethods of monitoring PSA are probes or primers which consist offragments of the PSA cDNA sequence. Illustrating this, primers used toPCR amplify a PSA polynucleotide must include less than the whole PSAsequence to function in the polymerase chain reaction. In the context ofsuch PCR reactions, skilled artisans generally create a variety ofdifferent polynucleotide fragments that can be used as primers in orderto amplify different portions of a polynucleotide of interest or tooptimize amplification reactions (see, e.g., Caetano-Anolles, G.Biotechniques 25(3): 472-476, 478-480 (1998); Robertson et al., MethodsMol. Biol. 98:121-154 (1998)). An additional illustration of the use ofsuch fragments is provided in Example 4, where a 238P1B2 polynucleotidefragment is used as a probe to show the expression of 238P1B2 RNAs incancer cells. In addition, variant polynucleotide sequences aretypically used as primers and probes for the corresponding mRNAs in PCRand Northern analyses (see, e.g., Sawai et al., Fetal Diagn. Ther. 1996November-December 11(6):407-13 and Current Protocols In MolecularBiology, Volume 2, Unit 2, Frederick M. Ausubel et al. eds., 1995)).Polynucleotide fragments and variants are useful in this context wherethey are capable of binding to a target polynucleotide sequence (e.g., a238P1B2 polynucleotide shown in FIG. 2 or variant thereof) underconditions of high stringency.

Furthermore, PSA polypeptides which contain an epitope that can berecognized by an antibody or T cell that specifically binds to thatepitope are used in methods of monitoring PSA. 238P1B2 polypeptidefragments and polypeptide analogs or variants can also be used in ananalogous manner. This practice of using polypeptide fragments orpolypeptide variants to generate antibodies (such as anti-PSA antibodiesor T cells) is typical in the art with a wide variety of systems such asfusion proteins being used by practitioners (see, e.g., CurrentProtocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubelet al. eds., 1995). In this context, each epitope(s) functions toprovide the architecture with which an antibody or T cell is reactive.Typically, skilled artisans create a variety of different polypeptidefragments that can be used in order to generate immune responsesspecific for different portions of a polypeptide of interest (see, e.g.,U.S. Pat. No. 5,840,501 and U.S. Pat. No. 5,939,533). For example it maybe preferable to utilize a polypeptide comprising one of the 238P1B2biological motifs discussed herein or a motif-bearing subsequence whichis readily identified by one of skill in the art based on motifsavailable in the art. Polypeptide fragments, variants or analogs aretypically useful in this context as long as they comprise an epitopecapable of generating an antibody or T cell specific for a targetpolypeptide sequence (e.g. a 238P1B2 polypeptide shown in FIG. 3).

As shown herein, the 238P1B2 polynucleotides and polypeptides (as wellas the 238P1B2 polynucleotide probes and anti-238P1B2 antibodies or Tcells used to identify the presence of these molecules) exhibit specificproperties that make them useful in diagnosing cancers such as thoselisted in Table I. Diagnostic assays that measure the presence of238P1B2 gene products, in order to evaluate the presence or onset of adisease condition described herein, such as prostate cancer, are used toidentify patients for preventive measures or further monitoring, as hasbeen done so successfully with PSA. Moreover, these materials satisfy aneed in the art for molecules having similar or complementarycharacteristics to PSA in situations where, for example, a definitediagnosis of metastasis of prostatic origin cannot be made on the basisof a test for PSA alone (see, e.g., Alanen et al., Pathol. Res. Pract.192(3): 233-237 (1996)), and consequently, materials such as 238P1B2polynucleotides and polypeptides (as well as the 238P1B2 polynucleotideprobes and anti-238P1B2 antibodies used to identify the presence ofthese molecules) need to be employed to confirm a metastases ofprostatic origin.

Finally, in addition to their use in diagnostic assays, the 238P1B2polynucleotides disclosed herein have a number of other utilities suchas their use in the identification of oncogenetic associated chromosomalabnormalities in the chromosomal region to which the 238P1B2 gene maps(see Example 3 below). Moreover, in addition to their use in diagnosticassays, the 238P1B2-related proteins and polynucleotides disclosedherein have other utilities such as their use in the forensic analysisof tissues of unknown origin (see, e.g., Takahama K Forensic Sci Int1996 Jun. 28; 80(1-2): 63-9).

Additionally, 238P1B2-related proteins or polynucleotides of theinvention can be used to treat a pathologic condition characterized bythe over-expression of 238P1B2. For example, the amino acid or nucleicacid sequence of FIG. 2 or FIG. 3, or fragments of either, can be usedto generate an immune response to a 238P1B2 antigen. Antibodies or othermolecules that react with 238P1B2 can be used to modulate the functionof this molecule, and thereby provide a therapeutic benefit.

XII.) Inhibition of 238P1B2 Protein Function

The invention includes various methods and compositions for inhibitingthe binding of 238P1B2 to its binding partner or its association withother protein(s) as well as methods for inhibiting 238P1B2 function.

XII.A.) Inhibition of 238P1B2 with Intracellular Antibodies

In one approach, a recombinant vector that encodes single chainantibodies that specifically bind to 238P1B2 are introduced into 238P1B2expressing cells via gene transfer technologies. Accordingly, theencoded single chain anti-238P1B2 antibody is expressed intracellularly,binds to 238P1B2 protein, and thereby inhibits its function. Methods forengineering such intracellular single chain antibodies are well known.Such intracellular antibodies, also known as “intrabodies”, arespecifically targeted to a particular compartment within the cell,providing control over where the inhibitory activity of the treatment isfocused. This technology has been successfully applied in the art (forreview, see Richardson and Marasco, 1995, TIBTECH vol. 13). Intrabodieshave been shown to virtually eliminate the expression of otherwiseabundant cell surface receptors (see, e.g., Richardson et al., 1995,Proc. Natl. Acad. Sci. USA 92: 3137-3141; Beerli et al., 1994, J. Biol.Chem. 289: 23931-23936; Deshane et al., 1994, Gene Ther. 1: 332-337).

Single chain antibodies comprise the variable domains of the heavy andlight chain joined by a flexible linker polypeptide, and are expressedas a single polypeptide. Optionally, single chain antibodies areexpressed as a single chain variable region fragment joined to the lightchain constant region. Well-known intracellular trafficking signals areengineered into recombinant polynucleotide vectors encoding such singlechain antibodies in order to precisely target the intrabody to thedesired intracellular compartment. For example, intrabodies targeted tothe endoplasmic reticulum (ER) are engineered to incorporate a leaderpeptide and, optionally, a C-terminal ER retention signal, such as theKDEL (SEQ ID: 5) amino acid motif. Intrabodies intended to exertactivity in the nucleus are engineered to include a nuclear localizationsignal. Lipid moieties are joined to intrabodies in order to tether theintrabody to the cytosolic side of the plasma membrane. Intrabodies canalso be targeted to exert function in the cytosol. For example,cytosolic intrabodies are used to sequester factors within the cytosol,thereby preventing them from being transported to their natural cellulardestination.

In one embodiment, intrabodies are used to capture 238P1B2 in thenucleus, thereby preventing its activity within the nucleus. Nucleartargeting signals are engineered into such 238P1B2 intrabodies in orderto achieve the desired targeting. Such 238P1B2 intrabodies are designedto bind specifically to a particular 238P1B2 domain. In anotherembodiment, cytosolic intrabodies that specifically bind to a 238P1B2protein are used to prevent 238P1B2 from gaining access to the nucleus,thereby preventing it from exerting any biological activity within thenucleus (e.g., preventing 238P1B2 from forming transcription complexeswith other factors).

In order to specifically direct the expression of such intrabodies toparticular cells, the transcription of the intrabody is placed under theregulatory control of an appropriate tumor-specific promoter and/orenhancer. In order to target intrabody expression specifically toprostate, for example, the PSA promoter and/or promoter/enhancer can beutilized (See, for example, U.S. Pat. No. 5,919,652 issued 6 Jul. 1999).

XII.B.) Inhibition of 238P1B2 with Recombinant Proteins

In another approach, recombinant molecules bind to 238P1B2 and therebyinhibit 238P1B2 function. For example, these recombinant moleculesprevent or inhibit 238P1B2 from accessing/binding to its bindingpartner(s) or associating with other protein(s). Such recombinantmolecules can, for example, contain the reactive part(s) of a 238P1B2specific antibody molecule. In a particular embodiment, the 238P1B2binding domain of a 238P1B2 binding partner is engineered into a dimericfusion protein, whereby the fusion protein comprises two 238P1B2 ligandbinding domains linked to the Fc portion of a human IgG, such as humanIgG1. Such IgG portion can contain, for example, the C_(H)2 and C_(H)3domains and the hinge region, but not the C_(H)1 domain. Such dimericfusion proteins are administered in soluble form to patients sufferingfrom a cancer associated with the expression of 238P1B2, whereby thedimeric fusion protein specifically binds to 238P1B2 and blocks 238P1B2interaction with a binding partner. Such dimeric fusion proteins arefurther combined into multimeric proteins using known antibody linkingtechnologies.

XII.C.) Inhibition of 238P1B2 Transcription or Translation

The present invention also comprises various methods and compositionsfor inhibiting the transcription of the 238P1B2 gene. Similarly, theinvention also provides methods and compositions for inhibiting thetranslation of 238P1B2 mRNA into protein.

In one approach, a method of inhibiting the transcription of the 238P1B2gene comprises contacting the 238P1B2 gene with a 238P1B2 antisensepolynucleotide. In another approach, a method of inhibiting 238P1B2 mRNAtranslation comprises contacting a 238P1B2 mRNA with an antisensepolynucleotide. In another approach, a 238P1B2 specific ribozyme is usedto cleave a 238P1B2 message, thereby inhibiting translation. Suchantisense and ribozyme based methods can also be directed to theregulatory regions of the 238P1B2 gene, such as 238P1B2 promoter and/orenhancer elements. Similarly, proteins capable of inhibiting a 238P1B2gene transcription factor are used to inhibit 238P1B2 mRNAtranscription. The various polynucleotides and compositions useful inthe aforementioned methods have been described above. The use ofantisense and ribozyme molecules to inhibit transcription andtranslation is well known in the art.

Other factors that inhibit the transcription of 238P1B2 by interferingwith 238P1B2 transcriptional activation are also useful to treat cancersexpressing 238P1B2. Similarly, factors that interfere with 238P1B2processing are useful to treat cancers that express 238P1B2. Cancertreatment methods utilizing such factors are also within the scope ofthe invention.

XII.D.) General Considerations for Therapeutic Strategies

Gene transfer and gene therapy technologies can be used to delivertherapeutic polynucleotide molecules to tumor cells synthesizing 238P1B2(i.e., antisense, ribozyme, polynucleotides encoding intrabodies andother 238P1B2 inhibitory molecules). A number of gene therapy approachesare known in the art. Recombinant vectors encoding 238P1B2 antisensepolynucleotides, ribozymes, factors capable of interfering with 238P1B2transcription, and so forth, can be delivered to target tumor cellsusing such gene therapy approaches.

The above therapeutic approaches can be combined with any one of a widevariety of surgical, chemotherapy or radiation therapy regimens. Thetherapeutic approaches of the invention can enable the use of reduceddosages of chemotherapy (or other therapies) and/or less frequentadministration, an advantage for all patients and particularly for thosethat do not tolerate the toxicity of the chemotherapeutic agent well.

The anti-tumor activity of a particular composition (e.g., antisense,ribozyme, intrabody), or a combination of such compositions, can beevaluated using various in vitro and in vivo assay systems. In vitroassays that evaluate therapeutic activity include cell growth assays,soft agar assays and other assays indicative of tumor promotingactivity, binding assays capable of determining the extent to which atherapeutic composition will inhibit the binding of 238P1B2 to a bindingpartner, etc.

In vivo, the effect of a 238P1B2 therapeutic composition can beevaluated in a suitable animal model. For example, xenogenic prostatecancer models can be used, wherein human prostate cancer explants orpassaged xenograft tissues are introduced into immune compromisedanimals, such as nude or SCID mice (Klein et al., 1997, Nature Medicine3: 402-408). For example, PCT Patent Application WO98/16628 and U.S.Pat. No. 6,107,540 describe various xenograft models of human prostatecancer capable of recapitulating the development of primary tumors,micrometastasis, and the formation of osteoblastic metastasescharacteristic of late stage disease. Efficacy can be predicted usingassays that measure inhibition of tumor formation, tumor regression ormetastasis, and the like.

In vivo assays that evaluate the promotion of apoptosis are useful inevaluating therapeutic compositions. In one embodiment, xenografts fromtumor bearing mice treated with the therapeutic composition can beexamined for the presence of apoptotic foci and compared to untreatedcontrol xenograft-bearing mice. The extent to which apoptotic foci arefound in the tumors of the treated mice provides an indication of thetherapeutic efficacy of the composition.

The therapeutic compositions used in the practice of the foregoingmethods can be formulated into pharmaceutical compositions comprising acarrier suitable for the desired delivery method. Suitable carriersinclude any material that when combined with the therapeutic compositionretains the anti-tumor function of the therapeutic composition and isgenerally non-reactive with the patient's immune system. Examplesinclude, but are not limited to, any of a number of standardpharmaceutical carriers such as sterile phosphate buffered salinesolutions, bacteriostatic water, and the like (see, generally,Remington's Pharmaceutical Sciences 16^(th) Edition, A. Osal., Ed.,1980).

Therapeutic formulations can be solubilized and administered via anyroute capable of delivering the therapeutic composition to the tumorsite. Potentially effective routes of administration include, but arenot limited to, intravenous, parenteral, intraperitoneal, intramuscular,intratumor, intradermal, intraorgan, orthotopic, and the like. Apreferred formulation for intravenous injection comprises thetherapeutic composition in a solution of preserved bacteriostatic water,sterile unpreserved water, and/or diluted in polyvinylchloride orpolyethylene bags containing 0.9% sterile Sodium Chloride for Injection,USP. Therapeutic protein preparations can be lyophilized and stored assterile powders, preferably under vacuum, and then reconstituted inbacteriostatic water (containing for example, benzyl alcoholpreservative) or in sterile water prior to injection.

Dosages and administration protocols for the treatment of cancers usingthe foregoing methods will vary with the method and the target cancer,and will generally depend on a number of other factors appreciated inthe art.

XIII.) Kits

For use in the diagnostic and therapeutic applications described herein,kits are also within the scope of the invention. Such kits can comprisea carrier, package or container that is compartmentalized to receive oneor more containers such as vials, tubes, and the like, each of thecontainer(s) comprising one of the separate elements to be used in themethod. For example, the container(s) can comprise a probe that is orcan be detectably labeled. Such probe can be an antibody orpolynucleotide specific for a 238P1B2-related protein or a 238P1B2 geneor message, respectively. Where the method utilizes nucleic acidhybridization to detect the target nucleic acid, the kit can also havecontainers containing nucleotide(s) for amplification of the targetnucleic acid sequence and/or a container comprising a reporter-means,such as a biotin-binding protein, such as avidin or streptavidin, boundto a reporter molecule, such as an enzymatic, florescent, orradioisotope label. The kit can include all or part of the amino acidsequence of FIG. 2 or FIG. 3 or analogs thereof, or a nucleic acidmolecules that encodes such amino acid sequences.

The kit of the invention will typically comprise the container describedabove and one or more other containers comprising materials desirablefrom a commercial and user standpoint, including buffers, diluents,filters, needles, syringes, and package inserts with instructions foruse.

A label can be present on the container to indicate that the compositionis used for a specific therapy or non-therapeutic application, and canalso indicate directions for either in vivo or in vitro use, such asthose described above. Directions and or other information can also beincluded on an insert which is included with the kit.

EXAMPLES

Various aspects of the invention are further described and illustratedby way of the several examples that follow, none of which are intendedto limit the scope of the invention.

Example 1 SSH-Generated Isolation of a cDNA Fragment of the 238P1B2 Gene

The Suppression Subtractive Hybridization (SSH) procedure using cDNAderived from patient cancer tissues is used to isolate genes that areover-expressed in cancer. The 238P1B2 SSH cDNA sequence was derived froma colon cancer pool minus normal tissue cDNA subtraction. Included inthe driver were cDNAs derived from 10 normal tissues. The 238P1B2 cDNAwas identified as highly expressed in the prostate cancer tissue pool,with restricted expression detected in normal tissues.

The SSH DNA sequence of 210 bp (FIG. 1) is novel but shows homology tomouse olfactory receptor MOR14-10 mRNA. A 238P1B2 cDNA, 238P1B2-clone A,of 3754 bp was isolated from prostate cDNA library, revealing an ORF of254 amino acids (FIG. 2, FIG. 3 and FIG. 4A).

Materials and Methods

Human Tissues:

The patient cancer and normal tissues were purchased from differentsources such as the NDRI (Philadelphia, Pa.). mRNA for some normaltissues were purchased from Clontech, Palo Alto, Calif.

RNA Isolation:

Tissues were homogenized in Trizol reagent (Life Technologies, GibcoBRL) using 10 ml/g tissue isolate total RNA. Poly A RNA was purifiedfrom total RNA using Qiagen's Oligotex mRNA Mini and Midi kits. Totaland mRNA were quantified by spectrophotometric analysis (O.D. 260/280nm) and analyzed by gel electrophoresis.

Oligonucleotides:

The following HPLC purified oligonucleotides were used.

DPNCDN (cDNA synthesis primer): (SEQ ID: 6) 5′TTTTGATCAAGCTT₃₀3′ Adaptor1: (SEQ ID: 7) 5′CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3′ (SEQ ID:8) 3′GGCCCGTCCTAG5′ Adaptor 2: (SEQ ID: 9)5′GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3′ (SEQ ID: 10) 3′CGGCTCCTAG5′PCR primer 1: (SEQ ID: 11) 5′CTAATACGACTCACTATAGGGC3′ Nested primer(NP)1: (SEQ ID: 12) 5′TCGAGCGGCCGCCCGGGCAGGA3′ Nested primer (NP)2: (SEQID: 13) 5′AGCGTGGTCGCGGCCGAGGA3′

Suppression Subtractive Hybridization:

Suppression Subtractive Hybridization (SSH) was used to identify cDNAscorresponding to genes that are differentially expressed in cancer. TheSSH reaction utilized cDNA from colon cancer and normal tissues.

The gene 238P1B2 sequence was derived from a colon cancer pool minusnormal tissue cDNA subtraction. The SSH DNA sequence (FIG. 1) wasidentified.

The cDNA derived from of a pool of normal tissues was used as the sourceof the “driver” cDNA, while the cDNA from a pool of patient cancertissues was used as the source of the “tester” cDNA. Double strandedcDNAs corresponding to tester and driver cDNAs were synthesized from 2μg of poly(A)⁺ RNA isolated from the relevant xenograft tissue, asdescribed above, using CLONTECH's PCR-Select cDNA Subtraction Kit and 1ng of oligonucleotide DPNCDN as primer. First- and second-strandsynthesis were carried out as described in the Kit's user manualprotocol (CLONTECH Protocol No. PT1117-1, Catalog No. K1804-1). Theresulting cDNA was digested with Dpn II for 3 hrs at 37° C. DigestedcDNA was extracted with phenol/chloroform (1:1) and ethanolprecipitated.

Driver cDNA was generated by combining in a 1:1 ratio Dpn II digestedcDNA from the relevant tissue source (see above) with a mix of digestedcDNAs derived from the nine normal tissues: stomach, skeletal muscle,lung, brain, liver, kidney, pancreas, small intestine, and heart.

Tester cDNA was generated by diluting 1 μl of Dpn II digested cDNA fromthe relevant tissue source (see above) (400 ng) in 5 μl of water. Thediluted cDNA (2 μl, 160 ng) was then ligated to 2 μl of Adaptor 1 andAdaptor 2 (10 μM), in separate ligation reactions, in a total volume of10 μl at 16° C. overnight, using 400 u of T4 DNA ligase (CLONTECH).Ligation was terminated with 1 μl of 0.2 M EDTA and heating at 72° C.for 5 min.

The first hybridization was performed by adding 1.5 μl (600 ng) ofdriver cDNA to each of two tubes containing 1.5 μl (20 ng) Adaptor 1-and Adaptor 2-ligated tester cDNA. In a final volume of 4 μl, thesamples were overlaid with mineral oil, denatured in an MJ Researchthermal cycler at 98° C. for 1.5 minutes, and then were allowed tohybridize for 8 hrs at 68° C. The two hybridizations were then mixedtogether with an additional 1 μl of fresh denatured driver cDNA and wereallowed to hybridize overnight at 68° C. The second hybridization wasthen diluted in 200 μl of 20 mM Hepes, pH 8.3, 50 mM NaCl, 0.2 mM EDTA,heated at 70° C. for 7 min. and stored at −20° C.

PCR Amplification, Cloning and Sequencing of Gene Fragments Generatedfrom SSH:

To amplify gene fragments resulting from SSH reactions, two PCRamplifications were performed. In the primary PCR reaction 1 μl of thediluted final hybridization mix was added to 1 μl of PCR primer 1 (10μM), 0.5 μl dNTP mix (10 μM), 2.5 μl 10× reaction buffer (CLONTECH) and0.5 μl 50× Advantage cDNA polymerase Mix (CLONTECH) in a final volume of25 μl. PCR 1 was conducted using the following conditions: 75° C. for 5min., 94° C. for 25 sec., then 27 cycles of 94° C. for 10 sec, 66° C.for 30 sec, 72° C. for 1.5 min. Five separate primary PCR reactions wereperformed for each experiment. The products were pooled and diluted 1:10with water. For the secondary PCR reaction, 1 μl from the pooled anddiluted primary PCR reaction was added to the same reaction mix as usedfor PCR 1, except that primers NP1 and NP2 (10 μM) were used instead ofPCR primer 1. PCR 2 was performed using 10-12 cycles of 94° C. for 10sec, 68° C. for 30 sec, and 72° C. for 1.5 minutes. The PCR productswere analyzed using 2% agarose gel electrophoresis.

The PCR products were inserted into pCR2.1 using the T/A vector cloningkit (Invitrogen). Transformed E. coli were subjected to blue/white andampicillin selection. White colonies were picked and arrayed into 96well plates and were grown in liquid culture overnight. To identifyinserts, PCR amplification was performed on 1 ml of bacterial cultureusing the conditions of PCR1 and NP1 and NP2 as primers. PCR productswere analyzed using 2% agarose gel electrophoresis.

Bacterial clones were stored in 20% glycerol in a 96 well format.Plasmid DNA was prepared, sequenced, and subjected to nucleic acidhomology searches of the GenBank, dBest, and NCI-CGAP databases.

RT-PCR Expression Analysis:

First strand cDNAs can be generated from 1 μg of mRNA with oligo(dT)12-18 priming using the Gibco-BRL Superscript Preamplificationsystem. The manufacturer's protocol was used which included anincubation for 50 min at 42° C. with reverse transcriptase followed byRNAse H treatment at 37° C. for 20 min. After completing the reaction,the volume can be increased to 200 μl with water prior to normalization.First strand cDNAs from 16 different normal human tissues can beobtained from Clontech.

Normalization of the first strand cDNAs from multiple tissues wasperformed by using the primers 5′atatcgccgcgctcgtcgtcgacaa3′ (SEQ ID:14) and 5′agccacacgcagctcattgtagaagg 3′ (SEQ ID: 15) to amplify β-actin.First strand cDNA (5 μl) were amplified in a total volume of 50 μlcontaining 0.4 μM primers, 0.2 μM each dNTPs, 1×PCR buffer (Clontech, 10mM Tris-HCL, 1.5 mM MgCl₂, 50 mM KCl, pH8.3) and 1× Klentaq DNApolymerase (Clontech). Five μl of the PCR reaction can be removed at 18,20, and 22 cycles and used for agarose gel electrophoresis. PCR wasperformed using an MJ Research thermal cycler under the followingconditions: Initial denaturation can be at 94° C. for 15 sec, followedby a 18, 20, and 22 cycles of 94° C. for 15, 65° C. for 2 min, 72° C.for 5 sec. A final extension at 72° C. was carried out for 2 min. Afteragarose gel electrophoresis, the band intensities of the 283 b.p.β-actin bands from multiple tissues were compared by visual inspection.Dilution factors for the first strand cDNAs were calculated to result inequal β-actin band intensities in all tissues after 22 cycles of PCR.Three rounds of normalization can be required to achieve equal bandintensities in all tissues after 22 cycles of PCR.

To determine expression levels of the 238P1B2 gene, 5 μl of normalizedfirst strand cDNA were analyzed by PCR using 26, and 30 cycles ofamplification. Semi-quantitative expression analysis can be achieved bycomparing the PCR products at cycle numbers that give light bandintensities. The primers used for RT-PCR were designed using the 238P1B2SSH sequence and are listed below:

238P1B2.1 5′-TTGCAGAATATCACCTCCACTTCC-3′ (SEQ ID: 16) 238P1B2.25′-GATCAGGCTGTTTCCCAAGAGAG-3′ (SEQ ID: 17)

A typical RT-PCR expression analysis is shown in FIG. 14. RT-PCRexpression analysis was performed on first strand cDNAs generated usingpools of tissues from multiple samples. The cDNAs were shown to benormalized using beta-actin PCR. Results show strong expression of238P1B2 in prostate cancer pool but not in vital pool 1 and vital pool2.

Example 2 Full Length Cloning of 238P1B2

The 238P1B2 SSH cDNA sequence was derived from a colon cancer pool minusnormal tissue cDNA subtraction. The SSH cDNA sequence (FIG. 1) wasdesignated 238P1B2.

The SSH DNA sequence of 210 bp (FIG. 1) is novel and shows 91% identityto mouse olfactory receptor MOR14-10 mRNA.

A full length cDNA (238P1B2-clone A) of 3754 bp was isolated fromprostate library, revealing an ORF of 254 amino acids (FIGS. 2 and 3).The cDNA shows highest homology to the mouse MOR-14-1 and MOR14-10olfactory receptors, with identities of 85% over 912 nucleotides and 83%over 906 nucleotides respectively (FIG. 4).

The protein sequence reveals 7 transmembrane domains and has homology toG protein-coupled receptors (GPCRs) involved in olfaction (Raming etal., 1993, Nature 361: 353; Malnic et al., 1999, Cell 96:713). Proteinsthat are members of this receptor family exhibit an extracellularamino-terminus, three additional extracellular loops, threeintracellular loops and an intracellular carboxyl terminus.

The most homologous sequence to 238P1B2 is mouse MOR14-1 protein. Thetwo proteins share 83% identity over a 253 amino acid region. Alignmentof the two proteins is shown in FIG. 4.

238P1B2 also shows significant homology to the prostate specific GPCR,PHOR-1. The two proteins share 48% identity over a region of 250 aminoacids (FIG. 4).

The full length 238P1B2 cDNA (238P1B2-clone A) was deposited with theAmerican Type Culture Collection on Mar. 7, 2002, and assigned accessionnumber PTA-4124.

238P1B2 v.1A protein sequence codes for a six transmembrane protein.Extension of the protein at the amino terminus adds another 62 aminoacids to 238P1B2 v.1A leading to 238P1B2 v.1B. This 62 amino acidterminus of 238P1B2 v.1B encodes an additional transmembrane region, andthereby making 238P1B2 v.1B a seven transmembrane protein. Furthermore,this amino terminus shows 84% identity to the mouse MOR14-10 G-coupledprotein receptor, indicating that this amino-terminal portion is encodedin nature.

The natural expression of 238P1B2 v.1B can occur if the stop siteupstream of the 62 amino acid extension is modified by single nucleicacid substitution leading to conversion of the stop codon into a codingamino acid. Polymorphisms can exist within different tissues, or betweendifferent individuals that mutate the stop codon, and therefore allowingproper translation of the 62 amino acid amino-terminal region of 238P1B2v.1B. Such a variation can either add a start methionine directly, orextend the coding region 238P1B2 v.1B for an additional 16 amino acidsuntil reaching a start methionine at nucleic acid position 1896.

Example 3 Chromosomal Mapping of 238P1B2 Gene

Chromosomal localization can implicate genes in disease pathogenesis.Several chromosome mapping approaches are available includingfluorescent in situ hybridization (FISH), human/hamster radiation hybrid(RH) panels (Walter et al., 1994; Nature Genetics 7:22; ResearchGenetics, Huntsville Ala.), human-rodent somatic cell hybrid panels suchas is available from the Coriell Institute (Camden, N.J.), and genomicviewers utilizing BLAST homologies to sequenced and mapped genomicclones (NCBI, Bethesda, Md.).

Using 238P1B2 sequence and the NCBI BLAST tool, placed 238P1B2 tochromosome 11p15.5, a region rich in GPCRs.

Because the human 238P1B2 gene maps to chromosome 11p15.5,polynucleotides encoding different regions of the 238P1B2 protein can beused to characterize cytogenetic abnormalities on chromosome 11, bandp15.5 that have been identified as being associated with variouscancers. In particular, a variety of chromosomal abnormalities in11p15.5 have been identified as frequent cytogenetic abnormalities in anumber of different cancers (see, e.g., Lai et al., 2000, Clin. CancerRes. 6(8):3172-6; Oya and Schulz, 2000, Br. J. Cancer 83(5):626-31;Svaren et al., Sep. 12, 2000, J. Biol. Chem.). Consequently,polynucleotides encoding specific regions of the 238P1B2 protein providenew tools that can be used to delineate, with greater precision thanpreviously possible, the specific nature of the cytogeneticabnormalities in this region of chromosome 11 that contribute to themalignant phenotype. In this context, these polynucleotides satisfy aneed in the art for expanding the sensitivity of chromosomal screeningin order to identify more subtle and less common chromosomalabnormalities (see, e.g., Evans et al., 1994, Am. J. Obstet. Gynecol.171(4):1055-1057).

Example 4 Expression Analysis of 238P1B2 in Normal Tissues and PatientSpecimens

Expression analysis by RT-PCR demonstrated that 238P1B2 is stronglyexpressed in prostate cancer patient specimens (FIG. 14). First strandcDNA was prepared from vital pool 1 (liver, lung and kidney), vital pool2 (pancreas, colon and stomach) and prostate cancer pool. Normalizationwas performed by PCR using primers to actin and GAPDH. Semi-quantitativePCR, using primers to 238P1B2, was performed at 26 and 30 cycles ofamplification. Results show strong expression of 238P1B2 in prostatecancer pool but not in vital pool 1 and vital pool 2.

Northern blot analysis of 238P1B2 in 16 human normal tissues is shown inFIG. 15. Results show absence of 238P1B2 expression in all 16 normaltissues tested. Extensive analysis of expression of 238P1B2 in 76 humantissues shows restricted expression of 238P1B2 in placenta (FIG. 16).

Expression of 238P1B2 in patient cancer specimens and human normaltissues is shown in FIG. 17. RNA was extracted from a pool of threeprostate cancers, as well as from normal prostate (NP), normal bladder(NB), normal kidney (NK), normal colon (NC), normal lung (NL) normalbreast (NBr) and normal ovary (NO). Northern blot with 10 μg of totalRNA/lane was probed with 238P1B2 sequence. The results show expressionof an approximately 4.5 kb 238P1B2 transcript in the prostate cancerpool and ovary but not in the other normal tissues tested. Analysis ofindividual patient specimens shows strong expression of 238P1B2 inprostate cancer tissues (FIG. 18). The expression for 238P1B2 detectedin tumors of Gleason score 7 is significantly stronger than theexpression detected in tumors of Gleason score 5. This result indicatesthat 238P1B2 can be used as a prognostic marker for prostate cancer.

The restricted expression of 238P1B2 in normal tissues and theexpression detected in prostate cancer suggest that 238P1B2 is apotential therapeutic target and a diagnostic marker for human cancers.

Example 5 Transcript Variants of 238P1B2

Transcript variants are variants of mature mRNA from the same gene byalternative transcription or alternative splicing. Alternativetranscripts are transcripts from the same gene that start transcriptionat different points. Splice variants are mRNA variants spliceddifferently from the same transcript. In eukaryotes, when a multi-exongene is transcribed from genomic DNA, the initial RNA is spliced toproduce functional mRNA, which has only exons and is used fortranslation into an amino acid sequence. Accordingly, a given gene canhave zero to many alternative transcripts and each transcript can havezero to many splice variants. Each transcript variant has a unique exonmakeup, and can have different coding and/or non-coding (5′ or 3′ end)portions, from the original transcript. Transcript variants can code forsimilar or different proteins with the same or a similar function or canencode proteins with different functions, and can be expressed in thesame tissue at the same time, or in different tissues at the same time,or in the same tissue at different times, or in different tissues atdifferent times. Proteins encoded by transcript variants can havesimilar or different cellular or extracellular localizations, e.g.,secreted versus intracellular.

Transcript variants are identified by a variety of art-accepted methods.For example, alternative transcripts and splice variants are identifiedby full-length cloning experiments, or by use of full-length transcriptand EST sequences. First, all human ESTs were grouped into clusterswhich show direct or indirect identity with each other. Second, ESTs inthe same cluster were further grouped into sub-clusters and assembledinto a consensus sequence. The original gene sequence is compared to theconsensus sequence(s) or other full-length sequences. Each consensussequence is a potential splice variant for that gene. Even when avariant is identified that is not a full-length clone, that portion ofthe variant is very useful for antigen generation and for furthercloning of the full-length splice variant, using techniques known in theart.

Moreover, computer programs are available in the art that identifytranscript variants based on genomic sequences. Genomic-based transcriptvariant identification programs include FgenesH (A. Salamov and V.Solovyev, “Ab initio gene finding in Drosophila genomic DNA,” GenomeResearch. 2000 April; 10(4):516-22); Grail and GenScan. For a generaldiscussion of splice variant identification protocols see., e.g.,Southan, C., A genomic perspective on human proteases, FEBS Lett. 2001Jun. 8; 498(2-3):214-8; de Souza, S. J., et al., Identification of humanchromosome 22 transcribed sequences with ORF expressed sequence tags,Proc. Natl. Acad Sci USA. 2000 Nov. 7; 97(23):12690-3.

To further confirm the parameters of a transcript variant, a variety oftechniques are available in the art, such as full-length cloning,proteomic validation, PCR-based validation, and 5′ RACE validation, etc.(see e.g., Proteomic Validation Brennan, S. O., et al., Albumin bankspeninsula: a new termination variant characterized by electrospray massspectrometry, Biochem Biophys Acta. 1999 Aug. 17; 1433(1-2):321-6;Ferranti P, et al., Differential splicing of pre-messenger RNA producesmultiple forms of mature caprine alpha(s1)-casein, Eur J. Biochem. 1997Oct. 1; 249(1):1-7. For PCR-based Validation: Wellmann S, et al.,Specific reverse transcription-PCR quantification of vascularendothelial growth factor (VEGF) splice variants by LightCyclertechnology, Clin Chem. 2001 April; 47(4):654-60; Jia, H. P., et al.,Discovery of new human beta-defensins using a genomics-based approach,Gene. 2001 Jan. 24; 263(1-2):211-8. For PCR-based and 5′ RACEValidation: Brigle, K. E., et al., Organization of the murine reducedfolate carrier gene and identification of variant splice forms, BiochemBiophys Acta. 1997 Aug. 7; 1353(2): 191-8).

It is known in the art that genomic regions are modulated in cancers.When the genomic region to which a gene maps is modulated in aparticular cancer, the alternative transcripts or splice variants of thegene are modulated as well. Disclosed herein is that 238P1B2 has aparticular expression profile. Alternative transcripts and splicevariants of 238P1B2 can share this expression pattern, thus serving astumor-associated markers/antigens.

The exon composition of the original transcript, designated as 238P1B2v.1, is shown in Table XXIII. No transcript variant has been identifiedby the above methods.

Example 6 Single Nucleotide Polymorphisms of 238P1B2

A Single Nucleotide Polymorphism (SNP) is a single base pair variationin a nucleotide sequence at a specific location. At any given point ofthe genome, there are four possible nucleotide base pairs: A/T, C/G, G/Cand T/A. Genotype refers to the specific base pair sequence of one ormore locations in the genome of an individual. Haplotype refers to thebase pair sequence of more than one location on the same DNA molecule(or the same chromosome in higher organisms), often in the context ofone gene or in the context of several tightly linked genes. SNPs thatoccur on a cDNA are called cSNPs. These cSNPs may change amino acids ofthe protein encoded by the gene and thus change the functions of theprotein. Some SNPs cause inherited diseases; others contribute toquantitative variations in phenotype and reactions to environmentalfactors including diet and drugs among individuals. Therefore, SNPsand/or combinations of alleles (called haplotypes) have manyapplications, including diagnosis of inherited diseases, determinationof drug reactions and dosage, identification of genes responsible fordiseases, and analysis of the genetic relationship between individuals(P. Nowotny, J. M. Kwon and A. M. Goate, “SNP analysis to dissect humantraits,” Curr. Opin. Neurobiol. 2001 October; 11(5):637-641; M.Pirmohamed and B. K. Park, “Genetic susceptibility to adverse drugreactions,” Trends Pharmacol. Sci. 2001 June; 22(6):298-305; J. H.Riley, C. J. Allan, E. Lai and A. Roses, “The use of single nucleotidepolymorphisms in the isolation of common disease genes,”Pharmacogenomics. 2000 February; 1(1):39-47; R. Judson, J. C. Stephensand A. Windemuth, “The predictive power of haplotypes in clinicalresponse,” Pharmacogenomics. 2000 February; 1(1):15-26).

SNPs are identified by a variety of art-accepted methods (P. Bean, “Thepromising voyage of SNP target discovery,” Am. Clin. Lab. 2001October-November; 20(9):18-20; K. M. Weiss, “In search of humanvariation,” Genome Res. 1998 July; 8(7):691-697; M. M. She, “Enablinglarge-scale pharmacogenetic studies by high-throughput mutationdetection and genotyping technologies,” Clin. Chem. 2001 February;47(2):164-172). For example, SNPs are identified by sequencing DNAfragments that show polymorphism by gel-based methods such asrestriction fragment length polymorphism (RFLP) and denaturing gradientgel electrophoresis (DGGE). They can also be discovered by directsequencing of DNA samples pooled from different individuals or bycomparing sequences from different DNA samples. With the rapidaccumulation of sequence data in public and private databases, one candiscover SNPs by comparing sequences using computer programs (Z. Gu, L.Hillier and P. Y. Kwok, “Single nucleotide polymorphism hunting incyberspace,” Hum. Mutat. 1998; 12(4):221-225). SNPs can be verified andgenotype or haplotype of an individual can be determined by a variety ofmethods including direct sequencing and high throughput microarrays (P.Y. Kwok, “Methods for genotyping single nucleotide polymorphisms,” Annu.Rev. Genomics Hum. Genet. 2001; 2:235-258; M. Kokoris, K. Dix, K.Moynihan, J. Mathis, B. Erwin, P. Grass, B. Hines and A. Duesterhoeft,“High-throughput SNP genotyping with the Masscode system,” Mol. Diagn.2000 December; 5(4):329-340).

38P1B2 SNPs are identified by direct sequencing of the cDNA clones andby comparison of those sequences with public and proprietary sequences.By comparing the sequences with high quality proprietary or publicsequences (e.g., NCBI/GenBank, accessible at World Wide Web URLncbi.nlm.nih.gov), five SNPs of 238P1B2 were identified at nucleotidepositions 274 (T/C), 1268 (T/G), 1299 (T/G) 2806 (T/C) and 3025 (T/C).The transcripts or proteins with alternative alleles were designated asvariants 238P1B2 v.2, v.3, v.4, v.5 and v.6. FIG. 10 shows the schematicalignment of the nucleotide variants. FIG. 11 shows the schematicalignment of protein variants, corresponding to nucleotide variants.Nucleotide variants that code for the same amino acid sequence asvariant 1 are not shown in FIG. 11. These alleles of the SNPs, thoughshown separately here, can occur in different combinations (haplotypes).

Example 7 Production of Recombinant 238P1B2 in Prokaryotic Systems

To express recombinant 238P1B2 in prokaryotic cells, the full or partiallength 238P1B2 variant 1a, variant 1b, and variant 2 cDNA sequences arecloned into any one of a variety of expression vectors known in the art.One or more of the following regions of 238P1B2 variants are expressedin these constructs: amino acids 1 to 254 of variant 1a; amino acids 1to 316 of variant 1b, and amino acids 1-254 of variant 2, or any 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50 or more contiguous amino acids from 238P1B2,variants, or analogs thereof.

A. In Vitro Transcription and Translation Constructs:

pCRII: To generate 238P1B2 sense and anti-sense RNA probes for RNA insitu investigations, pCRII constructs (Invitrogen, Carlsbad Calif.) aregenerated encoding either all of or fragments of the 238P1B2 cDNA. ThepCRII vector has Sp6 and T7 promoters flanking the insert to drive thetranscription of 238P1B2 RNA for use as probes in RNA in situhybridization experiments. These probes are used to analyze the cell andtissue expression of 238P1B2 at the RNA level. Transcribed 238P1B2 RNArepresenting the cDNA amino acid coding region of the 238P1B2 gene isused in in vitro translation systems such as the TnT™ CoupledReticulolysate System (Promega, Corp., Madison, Wis.) to synthesize238P1B2 protein.

B. Bacterial Constructs:

pGEX Constructs: To generate recombinant 238P1B2 proteins in bacteriathat are fused to the Glutathione S-transferase (GST) protein, all of orparts of the 238P1B2 cDNA protein coding sequence are fused to the GSTgene by cloning into pGEX-6P-1 or any other GST-fusion vector of thepGEX family (Amersham Pharmacia Biotech, Piscataway, N.J.). Theseconstructs allow controlled expression of recombinant 238P1B2 proteinsequences with GST fused at the amino-terminus and a six histidineepitope (6× His) at the carboxyl-terminus. The GST and 6× His tagspermit purification of the recombinant fusion protein from inducedbacteria with the appropriate affinity matrix and allow recognition ofthe fusion protein with anti-GST and anti-His antibodies. The 6× His tagis generated by adding 6 histidine codons to the cloning primer at the3′ end, e.g., of the open reading frame (ORF). A proteolytic cleavagesite, such as the PreScission™ recognition site in pGEX-6P-1, can beemployed to permit cleavage of the GST tag from 238P1B2-related protein.The ampicillin resistance gene and pBR322 origin permits selection andmaintenance of the pGEX plasmids in E. coli.

pMAL Constructs: To generate, in bacteria, recombinant 238P1B2 proteinsthat are fused to maltose-binding protein (MBP), all of or parts of the238P1B2 cDNA protein coding sequence are fused to the MBP gene bycloning into the pMAL-c2X and pMAL-p2X vectors (New England Biolabs,Beverly, Mass.). These constructs allow controlled expression ofrecombinant 238P1B2 protein sequences with MBP fused at theamino-terminus and a 6×His epitope tag at the carboxyl-terminus. The MBPand 6× His tags permit purification of the recombinant protein frominduced bacteria with the appropriate affinity matrix and allowrecognition of the fusion protein with anti-MBP and anti-His antibodies.The 6× His epitope tag is generated by adding 6 histidine codons to the3′ cloning primer. A Factor Xa recognition site permits cleavage of thepMAL tag from 238P1B2. The pMAL-c2X and pMAL-p2X vectors are optimizedto express the recombinant protein in the cytoplasm or periplasmrespectively. Periplasm expression enhances folding of proteins withdisulfide bonds.

pET Constructs: To express 238P1B2 in bacterial cells, all of or partsof the 238P1B2 cDNA protein coding sequence are cloned into the pETfamily of vectors (Novagen, Madison, Wis.). These vectors allow tightlycontrolled expression of recombinant 238P1B2 protein in bacteria withand without fusion to proteins that enhance solubility, such as NusA andthioredoxin (Trx), and epitope tags, such as 6× His and S-Tag™ that aidpurification and detection of the recombinant protein. For example,constructs are made utilizing pET NusA fusion system 43.1 such thatregions of the 238P1B2 protein are expressed as amino-terminal fusionsto NusA. In one embodiment, a NusA-fusion protein encompassing aminoacids 412-254 of 238P1B2 with a C-terminal 6× His tag was expressed inE. Coli, purified by metal chelate affinity chromatography, and used asan immunogen for generation of antibodies.

C. Yeast Constructs:

pESC Constructs: To express 238P1B2 in the yeast species Saccharomycescerevisiae for generation of recombinant protein and functional studies,all of or parts of the 238P1B2 cDNA protein coding sequence are clonedinto the pESC family of vectors each of which contain 1 of 4 selectablemarkers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La Jolla, Calif.).These vectors allow controlled expression from the same plasmid of up to2 different genes or cloned sequences containing either Flag™ or Mycepitope tags in the same yeast cell. This system is useful to confirmprotein-protein interactions of 238P1B2. In addition, expression inyeast yields similar post-translational modifications, such asglycosylations and phosphorylations, that are found when expressed ineukaryotic cells.

pESP Constructs: To express 238P1B2 in the yeast species Saccharomycespombe, all of or parts of the 238P1B2 cDNA protein coding sequence arecloned into the pESP family of vectors. These vectors allow controlledhigh level of expression of a 238P1B2 protein sequence that is fused ateither the amino terminus or at the carboxyl terminus to GST which aidspurification of the recombinant protein. A Flag™ epitope tag allowsdetection of the recombinant protein with anti-Flag™ antibody.

Example 8 Production of Recombinant 238P1B2 in Eukaryotic Systems

A. Mammalian Constructs:

To express recombinant 238P1B2 in eukaryotic cells, the full or partiallength 238P1B2 cDNA sequences can be cloned into any one of a variety ofexpression vectors known in the art. One or more of the followingregions of 238P1B2 are expressed in these constructs: amino acids 1 to254 of variant 1A or variant 2, amino acids 1 to 316 of variant 1B, orany 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50 or more contiguous amino acids from238P1B2, variants, or analogs thereof. In certain embodiments a regionof a specific variant of 238P1B2 is expressed that encodes an amino acidat a specific position which differs from the amino acid of any othervariant found at that position. In other embodiments, a region of avariant of 238P1B2 is expressed that lies partly or entirely within asequence that is unique to that variant.

The constructs can be transfected into any one of a wide variety ofmammalian cells such as 293T cells. Transfected 293T cell lysates can beprobed with the anti-238P1B2 polyclonal serum, described herein.

pcDNA4/HisMax Constructs: To express 238P1B2 in mammalian cells, a238P1B2 ORF, or portions thereof, of 238P1B2 are cloned intopcDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Proteinexpression is driven from the cytomegalovirus (CMV) promoter and theSP16 translational enhancer. The recombinant protein has Xpress™ and sixhistidine (6× His) epitopes fused to the amino-terminus. ThepcDNA4/HisMax vector also contains the bovine growth hormone (BGH)polyadenylation signal and transcription termination sequence to enhancemRNA stability along with the SV40 origin for episomal replication andsimple vector rescue in cell lines expressing the large T antigen. TheZeocin resistance gene allows for selection of mammalian cellsexpressing the protein and the ampicillin resistance gene and ColE1origin permits selection and maintenance of the plasmid in E. coli.

pcDNA3.1/MycHis Constructs: To express 238P1B2 in mammalian cells, a238P1B2 ORF, or portions thereof, of 238P1B2 with a consensus Kozaktranslation initiation site are cloned into pcDNA3.1/MycHis Version A(Invitrogen, Carlsbad, Calif.). Protein expression is driven from thecytomegalovirus (CMV) promoter. The recombinant proteins have the mycepitope and 6× His epitope fused to the carboxyl-terminus. ThepcDNA3.1/MycHis vector also contains the bovine growth hormone (BGH)polyadenylation signal and transcription termination sequence to enhancemRNA stability, along with the SV40 origin for episomal replication andsimple vector rescue in cell lines expressing the large T antigen. TheNeomycin resistance gene can be used, as it allows for selection ofmammalian cells expressing the protein and the ampicillin resistancegene and ColE1 origin permits selection and maintenance of the plasmidin E. coli.

pcDNA3.1/CT-GFP-TOPO Construct: To express 238P1B2 in mammalian cellsand to allow detection of the recombinant proteins using fluorescence, a238P1B2 ORF, or portions thereof, with a consensus Kozak translationinitiation site are cloned into pcDNA3.1/CT-GFP-TOPO (Invitrogen, CA).Protein expression is driven from the cytomegalovirus (CMV) promoter.The recombinant proteins have the Green Fluorescent Protein (GFP) fusedto the carboxyl-terminus facilitating non-invasive, in vivo detectionand cell biology studies. The pcDNA3.1CT-GFP-TOPO vector also containsthe bovine growth hormone (BGH) polyadenylation signal and transcriptiontermination sequence to enhance mRNA stability along with the SV40origin for episomal replication and simple vector rescue in cell linesexpressing the large T antigen. The Neomycin resistance gene allows forselection of mammalian cells that express the protein, and theampicillin resistance gene and ColE1 origin permits selection andmaintenance of the plasmid in E. coli. Additional constructs with anamino-terminal GFP fusion are made in pcDNA3.1/NT-GFP-TOPO spanning theentire length of a 238P1B2 protein.

PAPtag: A 238P1B2 ORF, or portions thereof, is cloned into pAPtag-5(GenHunter Corp. Nashville, Tenn.). This construct generates an alkalinephosphatase fusion at the carboxyl-terminus of a 238P1B2 protein whilefusing the IgGκ signal sequence to the amino-terminus. Constructs arealso generated in which alkaline phosphatase with an amino-terminal IgGκsignal sequence is fused to the amino-terminus of a 238P1B2 protein. Theresulting recombinant 238P1B2 proteins are optimized for secretion intothe media of transfected mammalian cells and can be used to identifyproteins such as ligands or receptors that interact with 238P1B2proteins. Protein expression is driven from the CMV promoter and therecombinant proteins also contain myc and 6× His epitopes fused at thecarboxyl-terminus that facilitates detection and purification. TheZeocin resistance gene present in the vector allows for selection ofmammalian cells expressing the recombinant protein and the ampicillinresistance gene permits selection of the plasmid in E. coli.

ptag5: A 238P1B2 ORF, or portions thereof, is cloned into pTag-5. Thisvector is similar to pAPtag but without the alkaline phosphatase fusion.This construct generates 238P1B2 protein with an amino-terminal IgGκsignal sequence and myc and 6× His epitope tags at the carboxyl-terminusthat facilitate detection and affinity purification. The resultingrecombinant 238P1B2 protein is optimized for secretion into the media oftransfected mammalian cells, and is used as immunogen or ligand toidentify proteins such as ligands or receptors that interact with the238P1B2 proteins. Protein expression is driven from the CMV promoter.The Zeocin resistance gene present in the vector allows for selection ofmammalian cells expressing the protein, and the ampicillin resistancegene permits selection of the plasmid in E. coli.

PsecFc: A 238P1B2 ORF, or portions thereof, is also cloned into psecFc.The psecFc vector was assembled by cloning the human immunoglobulin G1(IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen,California). This construct generates an IgG1 Fc fusion at thecarboxyl-terminus of the 238P1B2 proteins, while fusing the IgGK signalsequence to N-terminus. 238P1B2 fusions utilizing the murine IgG1 Fcregion are also used. The resulting recombinant 238P1B2 proteins areoptimized for secretion into the media of transfected mammalian cells,and can be used as immunogens or to identify proteins such as ligands orreceptors that interact with 238P1B2 protein. Protein expression isdriven from the CMV promoter. The hygromycin resistance gene present inthe vector allows for selection of mammalian cells that express therecombinant protein, and the ampicillin resistance gene permitsselection of the plasmid in E. coli.

pSRα Constructs: To generate mammalian cell lines that express 238P1B2constitutively, 238P1B2 ORF, or portions thereof, of 238P1B2 are clonedinto pSRα constructs. Amphotropic and ecotropic retroviruses aregenerated by transfection of pSRα constructs into the 293T-10A1packaging line or co-transfection of pSRα and a helper plasmid(containing deleted packaging sequences) into the 293 cells,respectively. The retrovirus is used to infect a variety of mammaliancell lines, resulting in the integration of the cloned gene, 238P1B2,into the host cell-lines. Protein expression is driven from a longterminal repeat (LTR). The Neomycin resistance gene present in thevector allows for selection of mammalian cells that express the protein,and the ampicillin resistance gene and ColE1 origin permit selection andmaintenance of the plasmid in E. coli. The retroviral vectors canthereafter be used for infection and generation of various cell linesusing, for example, PC3, NIH 3T3, TsuPr1, 293 or rat-1 cells.

Additional pSRα constructs are made that fuse an epitope tag such as theFLAG™ tag to the carboxyl-terminus of 238P1B2 sequences to allowdetection using anti-Flag antibodies. For example, the FLAG™ sequence 5′gat tac aag gat gac gac gat aag 3′ (SEQ ID: 18) is added to cloningprimer at the 3′ end of the ORF. Additional pSRα constructs are made toproduce both amino-terminal and carboxyl-terminal GFP and myc/6× Hisfusion proteins of the full-length 238P1B2 proteins.

Additional Viral Vectors: Additional constructs are made forviral-mediated delivery and expression of 238P1B2. High virus titerleading to high level expression of 238P1B2 is achieved in viraldelivery systems such as adenoviral vectors and herpes amplicon vectors.A 238P1B2 coding sequence or fragments thereof is amplified by PCR andsubcloned into the AdEasy shuttle vector (Stratagene). Recombination andvirus packaging are performed according to the manufacturer'sinstructions to generate adenoviral vectors. Alternatively, 238P1B2coding sequences or fragments thereof are cloned into the HSV-1 vector(Imgenex) to generate herpes viral vectors. The viral vectors arethereafter used for infection of various cell lines such as PC3, NIH3T3, 293 or rat-1 cells.

Regulated Expression Systems: To control expression of 238P1B2 inmammalian cells, coding sequences of 238P1B2, or portions thereof, arecloned into regulated mammalian expression systems such as the T-RexSystem (Invitrogen), the GeneSwitch System (Invitrogen) and thetightly-regulated Ecdysone System (Sratagene). These systems allow thestudy of the temporal and concentration dependent effects of recombinant238P1B2. These vectors are thereafter used to control expression of238P1B2 in various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.

B. Baculovirus Expression Systems

To generate recombinant 238P1B2 proteins in a baculovirus expressionsystem, 238P1B2 ORF, or portions thereof, are cloned into thebaculovirus transfer vector pBlueBac 4.5 (Invitrogen), which provides aHis-tag at the N-terminus. Specifically, pBlueBac-238P1B2 isco-transfected with helper plasmid pBac-N-Blue (Invitrogen) into SF9(Spodoptera frugiperda) insect cells to generate recombinant baculovirus(see Invitrogen instruction manual for details). Baculovirus is thencollected from cell supernatant and purified by plaque assay.

Recombinant 238P1B2 protein is then generated by infection of HighFiveinsect cells (Invitrogen) with purified baculovirus. Recombinant 238P1B2protein can be detected using anti-238P1B2 or anti-His-tag antibody.238P1B2 protein can be purified and used in various cell-based assays oras immunogen to generate polyclonal and monoclonal antibodies specificfor 238P1B2.

Example 9 Antigenicity Profiles and Secondary Structure

FIG. 5A,B, FIG. 6 A,B, FIG. 7 A,B, FIG. 8 A,B, and FIG. 9 A,B depictgraphically five amino acid profiles of the 238P1B2 variant 1a (5A-9a)amino acid sequence and variant 1b (5B-9B), each assessment available byaccessing the ProtScale website on the ExPasy molecular biology server.

These profiles: FIG. 5, Hydrophilicity, (Hopp T. P., Woods K. R., 1981.Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828); FIG. 6, Hydropathicity,(Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132); FIG. 7,Percentage Accessible Residues (Janin J., 1979 Nature 277:491-492); FIG.8, Average Flexibility, (Bhaskaran R., and Ponnuswamy P. K., 1988. Int.J. Pept. Protein Res. 32:242-255); FIG. 9, Beta-turn (Deleage, G., RouxB. 1987 Protein Engineering 1:289-294); and optionally others availablein the art, such as on the ProtScale website, were used to identifyantigenic regions of the 238P1B2 protein. Each of the above amino acidprofiles of 238P1B2 were generated using the following ProtScaleparameters for analysis: 1) A window size of 9; 2) 100% weight of thewindow edges compared to the window center; and, 3) amino acid profilevalues normalized to lie between 0 and 1.

Hydrophilicity (FIG. 5), Hydropathicity (FIG. 6) and PercentageAccessible Residues (FIG. 7) profiles were used to determine stretchesof hydrophilic amino acids (i.e., values greater than 0.5 on theHydrophilicity and Percentage Accessible Residues profile, and valuesless than 0.5 on the Hydropathicity profile). Such regions are likely tobe exposed to the aqueous environment, be present on the surface of theprotein, and thus be available for immune recognition, such as byantibodies.

Average Flexibility (FIG. 8) and Beta-turn (FIG. 9) profiles determinestretches of amino acids (i.e., values greater than 0.5 on the Beta-turnprofile and the Average Flexibility profile) that are not constrained insecondary structures such as beta sheets and alpha helices. Such regionsare also more likely to be exposed on the protein and thus accessiblefor immune recognition, such as by antibodies.

Antigenic sequences of the 238P1B2 variant 1a and variant 1b proteinindicated, e.g., by the profiles set forth in FIG. 5A,B, FIG. 6 A,B,FIG. 7 A,B, FIG. 8 A,B, and/or FIG. 9 A,B are used to prepareimmunogens, either peptides or nucleic acids that encode them, togenerate therapeutic and diagnostic anti-238P1B2 antibodies. Theimmunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more than 50contiguous amino acids, or the corresponding nucleic acids that encodethem, from the 238P1B2 variant proteins. In particular, peptideimmunogens for 238P1B2 variant 1a of the invention can comprise, apeptide region of at least 5 amino acids of FIG. 2 in any whole numberincrement up to 254 that includes an amino acid position having a valuegreater than 0.5 in the Hydrophilicity profile of FIG. 5A; a peptideregion of at least 5 amino acids of FIG. 2 in any whole number incrementup to 254 that includes an amino acid position having a value less than0.5 in the Hydropathicity profile of FIG. 6A; a peptide region of atleast 5 amino acids of FIG. 2 in any whole number increment up to 254that includes an amino acid position having a value greater than 0.5 inthe Percent Accessible Residues profile of FIG. 7A; a peptide region ofat least 5 amino acids of FIG. 2 in any whole number increment up to 254that includes an amino acid position having a value greater than 0.5 inthe Average Flexibility profile on FIG. 8A; and, a peptide region of atleast 5 amino acids of FIG. 2 in any whole number increment up to 254that includes an amino acid position having a value greater than 0.5 inthe Beta-turn profile of FIG. 9A.

In addition, peptide immunogens for 238P1B2 variant 1b of the inventioncan comprise, a peptide region of at least 5 amino acids of FIG. 2 inany whole number increment up to 316 that includes an amino acidposition having a value greater than 0.5 in the Hydrophilicity profileof FIG. 5B; a peptide region of at least 5 amino acids of FIG. 2 in anywhole number increment up to 316 that includes an amino acid positionhaving a value less than 0.5 in the Hydropathicity profile of FIG. 6B; apeptide region of at least 5 amino acids of FIG. 2 in any whole numberincrement up to 316 that includes an amino acid position having a valuegreater than 0.5 in the Percent Accessible Residues profile of FIG. 7B;a peptide region of at least 5 amino acids of FIG. 2 in any whole numberincrement up to 316 that includes an amino acid position having a valuegreater than 0.5 in the Average Flexibility profile on FIG. 8B; and, apeptide region of at least 5 amino acids of FIG. 2 in any whole numberincrement up to 316 that includes an amino acid position having a valuegreater than 0.5 in the Beta-turn profile of FIG. 9B. Immunogens of theinvention can also comprise nucleic acids that encode any of theforegoing peptides.

All immunogens of the invention, whether peptides or nucleic acids, canbe embodied in human unit dose form, or comprised by a composition thatincludes a pharmaceutical excipient compatible with human physiology.

The secondary structure of 238P1B2, namely the predicted presence andlocation of alpha helices, extended strands, and random coils, ispredicted from the primary amino acid sequence using theHNN-Hierarchical Neural Network method (Guermeur, 1997), accessed fromthe ExPasy molecular biology server. The analysis indicates that 238P1B2variant 1a is composed of 66.54% alpha helix, 6.69% extended strand, and26.77% random coil (FIG. 12A). The analysis indicates that 238P1B2variant 1b is composed of 61.71% alpha helix, 8.86% extended strand, and29.43% random coil (FIG. 12B).

Analysis for the potential presence of transmembrane domains in 238P1B2was carried out using a variety of transmembrane prediction algorithmsaccessed from the ExPasy molecular biology server. The programs predictthe presence of multiple transmembrane domains in 238P1B2 variant 1a andvariant 1b. The highest probability of topology for variant 1a is thatof a cell surface protein with 6 transmembrane domains. The highestprobability of topology for variant 1b is that of a cell surface proteinwith 7 transmembrane domains, consistent with that of a G-proteincoupled receptor. Shown graphically in FIG. 12C and FIG. 12D are theresults of analysis of 238P1B2 variant 1a using the TMpred (FIG. 12C)and TMHMM (FIG. 12D) prediction programs depicting the location andtopology of the 6 transmembrane domains. Shown in FIG. 12E and FIG. 12Fare the results of the prediction programs for 238P1B2 variant 1bshowing the location and topology of the 7 transmembrane domains. Theresults of each program, namely the amino acids encoding thetransmembrane domain, are summarized in Table XXII.

Example 10 Generation of 238P1B2 Polyclonal Antibodies

Polyclonal antibodies can be raised in a mammal, for example, by one ormore injections of an immunizing agent and, if desired, an adjuvant.Typically, the immunizing agent and/or adjuvant will be injected in themammal by multiple subcutaneous or intraperitoneal injections. Inaddition to immunizing with the full length 238P1B2 protein, computeralgorithms are employed in design of immunogens that, based on aminoacid sequence analysis contain characteristics of being antigenic andavailable for recognition by the immune system of the immunized host(see the Example entitled “Antigenicity Profiles”). Such regions wouldbe predicted to be hydrophilic, flexible, in beta-turn conformations,and/or be exposed on the surface of the protein (see, e.g., FIG. 5A,B,FIG. 6 A,B, FIG. 7 A,B, FIG. 8 A,B, and FIG. 9 A,B for amino acidprofiles that indicate such regions of 238P1B2 variants 1a and 1b).

For example, 238P1B2 recombinant bacterial fusion proteins or peptidescontaining hydrophilic, flexible, beta-turn regions of the 238P1B2variant 1, generally found in regions between transmembrane domains andat the amino and carboxyl termini, are used as antigens to generatepolyclonal antibodies in New Zealand White rabbits. Examples of suchregions include, but are not limited to, amino acids 30-43, amino acids109-141, and amino acids 208-211, which are regions that are predictedto be extracellular; and amino acids 67-85, amino acids 165-184, andamino acids 235-254, which are regions predicted to be intracellular. Inaddition, the amino-terminal region of variant 1b, amino acids 1-29 canbe used as an immunogen. Antibodies to this region are useful todistinguish variant 1b protein from variant 1a protein. It is useful toconjugate the immunizing agent to a protein known to be immunogenic inthe mammal being immunized. Examples of such immunogenic proteinsinclude, but are not limited to, keyhole limpet hemocyanin (KLH), serumalbumin, bovine thyroglobulin, and soybean trypsin inhibitor. In oneembodiment, a peptide encoding amino acids 1-29 of 238P1B2 variant 1b isconjugated to KLH and used to immunize the rabbit. Alternatively theimmunizing agent can include all or portions of the 238P1B2 protein,analogs or fusion proteins thereof. For example, the 238P1B2 amino acidsequence can be fused using recombinant DNA techniques to any one of avariety of fusion protein partners that are well known in the art, suchas glutathione-S-transferase (GST) and HIS tagged fusion proteins. Suchfusion proteins are purified from induced bacteria using the appropriateaffinity matrix.

In one embodiment, a GST-fusion protein encoding amino acids 1-254 ofvariant 1a is produced and purified and used as immunogen. Otherrecombinant bacterial fusion proteins that can be employed includemaltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulinconstant region (see the section entitled “Production of 238P1B2 inProkaryotic Systems” and Current Protocols In Molecular Biology, Volume2, Unit 16, Frederick M. Ausubul et al. eds., 1995; Linsley, P. S.,Brady, W., Urnes, M., Grosmaire, L., Damle, N., and Ledbetter, L. (1991)J. Exp. Med. 174, 561-566).

In addition to bacterial derived fusion proteins, mammalian expressedprotein antigens are also used. These antigens are expressed frommammalian expression vectors such as the Tag5 and Fc-fusion vectors (seethe section entitled “Production of Recombinant 238P1B2 in EukaryoticSystems”), and retain post-translational modifications such asglycosylations found in native protein. In one embodiment, amino acids109-141 of variant la are cloned into the Tag5 mammalian secretionvector. The recombinant protein is purified by metal chelatechromatography from tissue culture supernatants of 293T cells stablyexpressing the recombinant vector. The purified Tag5 238P1B2 protein isthen used as immunogen.

During the immunization protocol, it is useful to mix or emulsify theantigen in adjuvants that enhance the immune response of the hostanimal. Examples of adjuvants include, but are not limited to, completeFreund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A,synthetic trehalose dicorynomycolate).

In a typical protocol, rabbits are initially immunized subcutaneouslywith up to 200 μg, typically 100-200 μg, of fusion protein or peptideconjugated to KLH mixed in complete Freund's adjuvant (CFA). Rabbits arethen injected subcutaneously every two weeks with up to 200 μg,typically 100-200 μg, of the immunogen in incomplete Freund's adjuvant(IFA). Test bleeds are taken approximately 7-10 days following eachimmunization and used to monitor the titer of the antiserum by ELISA.

To test reactivity and specificity of immune serum, such as the rabbitserum derived from immunization with Tag5 238P1B2 variant 1a encodingamino acids 109-141, the full-length 238P1B2 cDNA is cloned into pCDNA3.1 myc-his expression vector (Invitrogen, see the Example entitled“Production of Recombinant 238P1B2 in Eukaryotic Systems”). Aftertransfection of the constructs into 293T cells, cell lysates are probedwith the anti-238P1B2 antibodies and with anti-His antibody (Santa CruzBiotechnologies, Santa Cruz, Calif.) to determine specific reactivity ofthe antibodies to denatured 238P1B2 protein using the Western blottechnique. Immunoprecipitation and flow cytometric analyses of 293T andother recombinant 238P1B2-expressing cells determine recognition ofnative protein by the antibodies. In addition, Western blot,immunoprecipitation, fluorescent microscopy, and flow cytometrictechniques using cells that endogenously express 238P1B2 are carried outto test specificity.

Anti-serum from rabbits immunized with 238P1B2 fusion proteins, such asGST and MBP fusion proteins, are purified by depletion of antibodiesreactive to the fusion partner sequence by passage over an affinitycolumn containing the fusion partner either alone or in the context ofan irrelevant fusion protein. For example, antiserum derived from aGST-238P1B2 fusion protein encoding amino acids 1-254 of variant 1a isfirst purified by passage over a column of GST protein covalentlycoupled to AffiGel matrix (BioRad, Hercules, Calif.). The antiserum isthen affinity purified by passage over a column composed of a MBP-fusionprotein also encoding amino acids 1-254 of variant 1a covalently coupledto Affigel matrix. The serum is then further purified by protein Gaffinity chromatography to isolate the IgG fraction. Sera from otherHis-tagged antigens and peptide immunized rabbits as well as fusionpartner depleted sera are affinity purified by passage over a columnmatrix composed of the original protein immunogen or free peptide.

Example 11 Generation of 238P1B2 Monoclonal Antibodies (mAbs)

In one embodiment, therapeutic mAbs to 238P1B2 comprise those that reactwith epitopes of the protein that would disrupt or modulate thebiological function of 238P1B2, for example antibodies that disrupt itsinteraction with ligands and binding partners. Therapeutic mAbs alsocomprise those that specifically bind epitopes of 238P1B2 exposed on thecell surface and thus are useful in targeting mAb-toxin conjugates.Immunogens for generation of such mAbs include those designed to encodeor contain the entire 238P1B2 protein, regions of the 238P1B2 proteinpredicted to be antigenic from computer analysis of the amino acidsequence (see, e.g., FIG. 5A,B, FIG. 6A,B, FIG. 7A,B, FIG. 8A,B, or FIG.9A,B, and the Example entitled “Antigenicity Profiles”), and regionssuch as predicted extracellular domains. Immunogens include peptides,recombinant bacterial proteins, and mammalian expressed Tag 5 proteinsand human and murine IgG FC fusion proteins. In addition, cellsexpressing high levels of 238P1B2, such as 293T-238P1B2 or300.19-238P1B2 murine Pre-B cells, are used to immunize mice.

To generate mAbs to 238P1B2, mice are first immunized intraperitoneally(IP) with, typically, 10-50 μg of protein immunogen or 10⁷238P1B2-expressing cells mixed in complete Freund's adjuvant. Mice arethen subsequently immunized IP every 2-4 weeks with, typically, 10-50 μgof protein immunogen or 10⁷ cells mixed in incomplete Freund's adjuvant.Alternatively, MPL-TDM adjuvant is used in immunizations. In addition tothe above protein and cell-based immunization strategies, a DNA-basedimmunization protocol is employed in which a mammalian expression vectorencoding 238P1B2 sequence is used to immunize mice by direct injectionof the plasmid DNA. For example, amino acids 109-141 is cloned into theTag5 mammalian secretion vector and the recombinant vector is used asimmunogen. In another example the same amino acids are cloned into anFc-fusion secretion vector in which the 238P1B2 sequence is fused at theamino-terminus to an IgK leader sequence and at the carboxyl-terminus tothe coding sequence of the human or murine IgG Fc region. Thisrecombinant vector is then used as immunogen. The plasmid immunizationprotocols are used in combination with purified proteins expressed fromthe same vector and with cells expressing 238P1B2.

During the immunization protocol, test bleeds are taken 7-10 daysfollowing an injection to monitor titer and specificity of the immuneresponse. Once appropriate reactivity and specificity is obtained asdetermined by ELISA, Western blotting, immunoprecipitation, fluorescencemicroscopy, and flow cytometric analyses, fusion and hybridomageneration is then carried out with established procedures well known inthe art (see, e.g., Harlow and Lane, 1988).

In one embodiment for generating 238P1B2 monoclonal antibodies, aTag5-238P1B2 antigen encoding amino acids 109-141 of variant 1a, apredicted extracellular domain, is expressed and purified from stablytransfected 293T cells. Balb C mice are initially immunizedintraperitoneally with 25 μg of the Tag5-238P1B2 protein mixed incomplete Freund's adjuvant. Mice are subsequently immunized every twoweeks with 25 μg of the antigen mixed in incomplete Freund's adjuvantfor a total of three immunizations. ELISA using the Tag5 antigendetermines the titer of serum from immunized mice. Reactivity andspecificity of serum to full length 238P1B2 protein is monitored byWestern blotting, immunoprecipitation and flow cytometry using 293Tcells transfected with an expression vector encoding the 238P1B2 cDNA(see e.g., the Example entitled “Production of Recombinant 238P1B2 inEukaryotic Systems”). Other recombinant 238P1B2-expressing cells orcells endogenously expressing 238P1B2 are also used. Mice showing thestrongest reactivity are rested and given a final injection of Tag5antigen in PBS and then sacrificed four days later. The spleens of thesacrificed mice are harvested and fused to SPO/2 myeloma cells usingstandard procedures (Harlow and Lane, 1988). Supernatants from HATselected growth wells are screened by ELISA, Western blot,immunoprecipitation, fluorescent microscopy, and flow cytometry toidentify 238P1B2 specific antibody-producing clones.

The binding affinity of a 238P1B2 monoclonal antibody is determinedusing standard technologies. Affinity measurements quantify the strengthof antibody to epitope binding and are used to help define which 238P1B2monoclonal antibodies are suitable for diagnostic or therapeutic use, asappreciated by one of skill in the art. The BIAcore system (Uppsala,Sweden) is a useful method for determining binding affinity. The BIAcoresystem uses surface plasmon resonance (SPR, Welford K. 1991, Opt. Quant.Elect. 23: 1; Morton and Myszka, 1998, Methods in Enzymology 295: 268)to monitor biomolecular interactions in real time. BIAcore analysisconveniently generates association rate constants, dissociation rateconstants, equilibrium dissociation constants, and affinity constants.

Example 12 HLA Class I and Class II Binding Assays

HLA class I and class II binding assays using purified HLA molecules areperformed in accordance with disclosed protocols (e.g., PCT publicationsWO 94/20127 and WO 94/03205; Sidney et al., Current Protocols inImmunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995);Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, purified MHCmolecules (5 to 500 nM) are incubated with various unlabeled peptideinhibitors and 1-10 nM ¹²⁵I-radiolabeled probe peptides as described.Following incubation, MHC-peptide complexes are separated from freepeptide by gel filtration and the fraction of peptide bound isdetermined. Typically, in preliminary experiments, each MHC preparationis titered in the presence of fixed amounts of radiolabeled peptides todetermine the concentration of HLA molecules necessary to bind 10-20% ofthe total radioactivity. All subsequent inhibition and direct bindingassays are performed using these HLA concentrations.

Since under these conditions [label]<[HLA] and IC₅₀≧[HLA], the measuredIC₅₀ values are reasonable approximations of the true K_(D) values.Peptide inhibitors are typically tested at concentrations ranging from120 μg/ml to 1.2 ng/ml, and are tested in two to four completelyindependent experiments. To allow comparison of the data obtained indifferent experiments, a relative binding Figure is calculated for eachpeptide by dividing the IC₅₀ of a positive control for inhibition by theIC₅₀ for each tested peptide (typically unlabeled versions of theradiolabeled probe peptide). For database purposes, and inter-experimentcomparisons, relative binding values are compiled. These values cansubsequently be converted back into IC₅₀ nM values by dividing the IC₅₀nM of the positive controls for inhibition by the relative binding ofthe peptide of interest. This method of data compilation is accurate andconsistent for comparing peptides that have been tested on differentdays, or with different lots of purified MHC.

Binding assays as outlined above may be used to analyze HLA supermotifand/or HLA motif-bearing peptides.

Example 13 Identification of HLA Supermotif- and Motif-Bearing CTLCandidate Epitopes

HLA vaccine compositions of the invention can include multiple epitopes.The multiple epitopes can comprise multiple HLA supermotifs or motifs toachieve broad population coverage. This example illustrates theidentification and confirmation of supermotif- and motif-bearingepitopes for the inclusion in such a vaccine composition. Calculation ofpopulation coverage is performed using the strategy described below.

Computer Searches and Algorithms for Identification of Supermotif and/orMotif-Bearing Epitopes

The searches performed to identify the motif-bearing peptide sequencesin the Example entitled “Antigenicity Profiles” and Tables V-XVIII andTable XIX, employ the protein sequence data from the gene product of238P1B2 set forth in FIGS. 2 and 3.

Computer searches for epitopes bearing HLA Class I or Class IIsupermotifs or motifs are performed as follows. All translated 238P1B2protein sequences are analyzed using a text string search softwareprogram to identify potential peptide sequences containing appropriateHLA binding motifs; such programs are readily produced in accordancewith information in the art in view of known motif/supermotifdisclosures. Furthermore, such calculations can be made mentally.

Identified A2-, A3-, and DR-supermotif sequences are scored usingpolynomial algorithms to predict their capacity to bind to specificHLA-Class I or Class II molecules. These polynomial algorithms accountfor the impact of different amino acids at different positions, and areessentially based on the premise that the overall affinity (or ΔG) ofpeptide-HLA molecule interactions can be approximated as a linearpolynomial function of the type:

“ΔG”=a _(1i) ×a _(2i) ×a _(3i) . . . ×a _(ni)

where a_(ji) is a coefficient which represents the effect of thepresence of a given amino acid (j) at a given position (i) along thesequence of a peptide of n amino acids. The crucial assumption of thismethod is that the effects at each position are essentially independentof each other (i.e., independent binding of individual side-chains).When residue j occurs at position i in the peptide, it is assumed tocontribute a constant amount j_(i) to the free energy of binding of thepeptide irrespective of the sequence of the rest of the peptide.

The method of derivation of specific algorithm coefficients has beendescribed in Gulukota et al., J. Mol. Biol. 267:1258-126, 1997; (seealso Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al.,J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchorand non-anchor alike, the geometric mean of the average relative binding(ARB) of all peptides carrying j is calculated relative to the remainderof the group, and used as the estimate of j_(i). For Class II peptides,if multiple alignments are possible, only the highest scoring alignmentis utilized, following an iterative procedure. To calculate an algorithmscore of a given peptide in a test set, the ARB values corresponding tothe sequence of the peptide are multiplied. If this product exceeds achosen threshold, the peptide is predicted to bind. Appropriatethresholds are chosen as a function of the degree of stringency ofprediction desired.

Selection of HLA-A2 Supertype Cross-Reactive Peptides

Protein sequences from 238P1B2 are scanned utilizing motifidentification software, to identify 8-, 9-10- and 11-mer sequencescontaining the HLA-A2-supermotif main anchor specificity. Typically,these sequences are then scored using the protocol described above andthe peptides corresponding to the positive-scoring sequences aresynthesized and tested for their capacity to bind purified HLA-A*0201molecules in vitro (HLA-A*0201 is considered a prototype A2 supertypemolecule).

These peptides are then tested for the capacity to bind to additionalA2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). Peptidesthat bind to at least three of the five A2-supertype alleles tested aretypically deemed A2-supertype cross-reactive binders. Preferred peptidesbind at an affinity equal to or less than 500 nM to three or more HLA-A2supertype molecules.

Selection of HLA-A3 Supermotif-Bearing Epitopes

The 238P1B2 protein sequence(s) scanned above is also examined for thepresence of peptides with the HLA-A3-supermotif primary anchors.Peptides corresponding to the HLA A3 supermotif-bearing sequences arethen synthesized and tested for binding to HLA-A*0301 and HLA-A*1101molecules, the molecules encoded by the two most prevalent A3-supertypealleles. The peptides that bind at least one of the two alleles withbinding affinities of ≦500 nM, often ≦200 nM, are then tested forbinding cross-reactivity to the other common A3-supertype alleles (e.g.,A*3101, A*3301, and A*6801) to identify those that can bind at leastthree of the five HLA-A3-supertype molecules tested.

Selection of HLA-B7 Supermotif Bearing Epitopes

The 238P1B2 protein(s) scanned above is also analyzed for the presenceof 8-, 9- 10-, or 11-mer peptides with the HLA-B7-supermotif.Corresponding peptides are synthesized and tested for binding toHLA-B*0702, the molecule encoded by the most common B7-supertype allele(i.e., the prototype B7 supertype allele). Peptides binding B*0702 withIC₅₀ of ≦500 nM are identified using standard methods. These peptidesare then tested for binding to other common B7-supertype molecules(e.g., B*3501, B*5101, B*5301, and B*5401). Peptides capable of bindingto three or more of the five B7-supertype alleles tested are therebyidentified.

Selection of A1 and A24 Motif-Bearing Epitopes

To further increase population coverage, HLA-A1 and -A24 epitopes canalso be incorporated into vaccine compositions. An analysis of the238P1B2 protein can also be performed to identify HLA-A1- andA24-motif-containing sequences.

High affinity and/or cross-reactive binding epitopes that bear othermotif and/or supermotifs are identified using analogous methodology.

Example 14 Confirmation of Immunogenicity

Cross-reactive candidate CTL A2-supermotif-bearing peptides that areidentified as described herein are selected to confirm in vitroimmunogenicity. Confirmation is performed using the followingmethodology:

Target Cell Lines for Cellular Screening:

The 0.221A2.1 cell line, produced by transferring the HLA-A2.1 gene intothe HLA-A, -B, -C null mutant human B-lymphoblastoid cell line 721.221,is used as the peptide-loaded target to measure activity ofHLA-A2.1-restricted CTL. This cell line is grown in RPMI-1640 mediumsupplemented with antibiotics, sodium pyruvate, nonessential amino acidsand 10% (v/v) heat inactivated FCS. Cells that express an antigen ofinterest, or transfectants comprising the gene encoding the antigen ofinterest, can be used as target cells to confirm the ability ofpeptide-specific CTLs to recognize endogenous antigen.

Primary CTL Induction Cultures:

Generation of Dendritic Cells (DC): PBMCs are thawed in RPMI with 30μg/ml DNAse, washed twice and resuspended in complete medium (RPMI-1640plus 5% AB human serum, non-essential amino acids, sodium pyruvate,L-glutamine and penicillin/streptomycin). The monocytes are purified byplating 10×10⁶ PBMC/well in a 6-well plate. After 2 hours at 37° C., thenon-adherent cells are removed by gently shaking the plates andaspirating the supernatants. The wells are washed a total of three timeswith 3 ml RPMI to remove most of the non-adherent and loosely adherentcells. Three ml of complete medium containing 50 ng/ml of GM-CSF and1,000 U/ml of IL-4 are then added to each well. TNFα is added to the DCson day 6 at 75 ng/ml and the cells are used for CTL induction cultureson day 7.

Induction of CTL with DC and Peptide: CD8+ T-cells are isolated bypositive selection with Dynal immunomagnetic beads (Dynabeads® M-450)and the Detacha-Bead® reagent. Typically about 200-250×10⁶ PBMC areprocessed to obtain 24×10⁶ CD8′ T-cells (enough for a 48-well plateculture). Briefly, the PBMCs are thawed in RPMI with 30 μg/ml DNAse,washed once with PBS containing 1% human AB serum and resuspended inPBS/1% AB serum at a concentration of 20×10⁶ cells/ml. The magneticbeads are washed 3 times with PBS/AB serum, added to the cells (140 μlbeads/20×10⁶ cells) and incubated for 1 hour at 4° C. with continuousmixing. The beads and cells are washed 4× with PBS/AB serum to removethe nonadherent cells and resuspended at 100×10⁶ cells/ml (based on theoriginal cell number) in PBS/AB serum containing 100 μl/ml Detacha-Bead®reagent and 30 μg/ml DNAse. The mixture is incubated for 1 hour at roomtemperature with continuous mixing. The beads are washed again withPBS/AB/DNAse to collect the CD8+ T-cells. The DC are collected andcentrifuged at 1300 rpm for 5-7 minutes, washed once with PBS with 1%BSA, counted and pulsed with 40 μg/ml of peptide at a cell concentrationof 1−2×10⁶/ml in the presence of 3 μg/ml β₂-microglobulin for 4 hours at20° C. The DC are then irradiated (4,200 rads), washed 1 time withmedium and counted again.

Setting up induction cultures: 0.25 ml cytokine-generated DC (at 1×10⁵cells/ml) are co-cultured with 0.25 ml of CD8+ T-cells (at 2×10⁶cell/ml) in each well of a 48-well plate in the presence of 10 ng/ml ofIL-7. Recombinant human IL-10 is added the next day at a finalconcentration of 10 ng/ml and rhuman IL-2 is added 48 hours later at 10IU/ml.

Restimulation of the induction cultures with peptide-pulsed adherentcells: Seven and fourteen days after the primary induction, the cellsare restimulated with peptide-pulsed adherent cells. The PBMCs arethawed and washed twice with RPMI and DNAse. The cells are resuspendedat 5×10⁶ cells/ml and irradiated at ˜4200 rads. The PBMCs are plated at2×10⁶ in 0.5 ml complete medium per well and incubated for 2 hours at37° C. The plates are washed twice with RPMI by tapping the plate gentlyto remove the nonadherent cells and the adherent cells pulsed with 10μg/ml of peptide in the presence of 3 μg/ml β₂ microglobulin in 0.25 mlRPMI/5% AB per well for 2 hours at 37° C. Peptide solution from eachwell is aspirated and the wells are washed once with RPMI. Most of themedia is aspirated from the induction cultures (CD8+ cells) and broughtto 0.5 ml with fresh media. The cells are then transferred to the wellscontaining the peptide-pulsed adherent cells. Twenty four hours laterrecombinant human IL-10 is added at a final concentration of 10 ng/mland recombinant human IL2 is added the next day and again 2-3 days laterat 50 IU/ml (Tsai et al., Critical Reviews in Immunology 18(1-2):65-75,1998). Seven days later, the cultures are assayed for CTL activity in a⁵¹Cr release assay. In some experiments the cultures are assayed forpeptide-specific recognition in the in situ IFNγ ELISA at the time ofthe second restimulation followed by assay of endogenous recognition 7days later. After expansion, activity is measured in both assays for aside-by-side comparison.

Measurement of CTL Lytic Activity by ⁵¹Cr Release.

Seven days after the second restimulation, cytotoxicity is determined ina standard (5 hr) ⁵¹Cr release assay by assaying individual wells at asingle E:T. Peptide-pulsed targets are prepared by incubating the cellswith 10 μg/ml peptide overnight at 37° C.

Adherent target cells are removed from culture flasks with trypsin-EDTA.Target cells are labeled with 200 μCi of ⁵¹Cr sodium chromate (Dupont,Wilmington, Del.) for 1 hour at 37° C. Labeled target cells areresuspended at 10⁶ per ml and diluted 1:10 with K562 cells at aconcentration of 3.3×10⁶/ml (an NK-sensitive erythroblastoma cell lineused to reduce non-specific lysis). Target cells (100 μl) and effectors(100 μl) are plated in 96 well round-bottom plates and incubated for 5hours at 37° C. At that time, 100 μl of supernatant are collected fromeach well and percent lysis is determined according to the formula:

[(cpm of the test sample−cpm of the spontaneous ⁵¹Cr releasesample)/(cpm of the maximal ⁵¹Cr release sample−cpm of the spontaneous⁵¹Cr release sample)]×100.

Maximum and spontaneous release are determined by incubating the labeledtargets with 1% Triton X-100 and media alone, respectively. A positiveculture is defined as one in which the specific lysis(sample-background) is 10% or higher in the case of individual wells andis 15% or more at the two highest E:T ratios when expanded cultures areassayed.

In Situ Measurement of Human IFNγ Production as an Indicator ofPeptide-Specific and Endogenous Recognition

Immulon 2 plates are coated with mouse anti-human IFNγ monoclonalantibody (4 μg/ml 0.1M NaHCO₃, pH8.2) overnight at 4° C. The plates arewashed with Ca²⁺, Mg²⁺-free PBS/0.05% Tween 20 and blocked with PBS/10%FCS for two hours, after which the CTLs (100 μl/well) and targets (100μl/well) are added to each well, leaving empty wells for the standardsand blanks (which received media only). The target cells, eitherpeptide-pulsed or endogenous targets, are used at a concentration of1×10⁶ cells/ml. The plates are incubated for 48 hours at 37° C. with 5%CO₂.

Recombinant human IFN-gamma is added to the standard wells starting at400 pg or 1200 pg/100 microliter/well and the plate incubated for twohours at 37° C. The plates are washed and 100 μl of biotinylated mouseanti-human IFN-gamma monoclonal antibody (2 microgram/ml in PBS/3%FCS/0.05% Tween 20) are added and incubated for 2 hours at roomtemperature. After washing again, 100 microliter HRP-streptavidin(1:4000) are added and the plates incubated for one hour at roomtemperature. The plates are then washed 6× with wash buffer, 100microliter/well developing solution (TMB 1:1) are added, and the platesallowed to develop for 5-15 minutes. The reaction is stopped with 50microliter/well 1M H₃PO₄ and read at OD450. A culture is consideredpositive if it measured at least 50 pg of IFN-gamma/well abovebackground and is twice the background level of expression.

CTL Expansion.

Those cultures that demonstrate specific lytic activity againstpeptide-pulsed targets and/or tumor targets are expanded over a two weekperiod with anti-CD3. Briefly, 5×10⁴ CD8+ cells are added to a T25 flaskcontaining the following: 1×10⁶ irradiated (4,200 rad) PBMC (autologousor allogeneic) per ml, 2×10⁵ irradiated (8,000 rad) EBV-transformedcells per ml, and OKT3 (anti-CD3) at 30 ng per ml in RPMI-1640containing 10% (v/v) human AB serum, non-essential amino acids, sodiumpyruvate, 25 μM 2-mercaptoethanol, L-glutamine andpenicillin/streptomycin. Recombinant human IL2 is added 24 hours laterat a final concentration of 200 IU/ml and every three days thereafterwith fresh media at 50 IU/ml. The cells are split if the cellconcentration exceeds 1×10⁶/ml and the cultures are assayed between days13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the ⁵¹Cr release assayor at 1×10⁶/ml in the in situ IFNγ assay using the same targets asbefore the expansion.

Cultures are expanded in the absence of anti-CD3⁺ as follows. Thosecultures that demonstrate specific lytic activity against peptide andendogenous targets are selected and 5×10⁴ CD8′ cells are added to a T25flask containing the following: 1×10⁶ autologous PBMC per ml which havebeen peptide-pulsed with 10 μg/ml peptide for two hours at 37° C. andirradiated (4,200 rad); 2×10⁵ irradiated (8,000 rad) EBV-transformedcells per ml RPMI-1640 containing 10% (v/v) human AB serum,non-essential AA, sodium pyruvate, 25 mM 2-ME, L-glutamine andgentamicin.

Immunogenicity of A2 Supermotif-Bearing Peptides

A2-supermotif cross-reactive binding peptides are tested in the cellularassay for the ability to induce peptide-specific CTL in normalindividuals. In this analysis, a peptide is typically considered to bean epitope if it induces peptide-specific CTLs in at least individuals,and preferably, also recognizes the endogenously expressed peptide.

Immunogenicity can also be confirmed using PBMCs isolated from patientsbearing a tumor that expresses 238P1B2. Briefly, PBMCs are isolated frompatients, re-stimulated with peptide-pulsed monocytes and assayed forthe ability to recognize peptide-pulsed target cells as well astransfected cells endogenously expressing the antigen.

Evaluation of A*03/A11 Immunogenicity

HLA-A3 supermotif-bearing cross-reactive binding peptides are alsoevaluated for immunogenicity using methodology analogous for that usedto evaluate the immunogenicity of the HLA-A2 supermotif peptides.

Evaluation of B7 Immunogenicity

Immunogenicity screening of the B7-supertype cross-reactive bindingpeptides identified as set forth herein are confirmed in a manneranalogous to the confirmation of A2- and A3-supermotif-bearing peptides.

Peptides bearing other supermotifs/motifs, e.g., HLA-A1, HLA-A24 etc.are also confirmed using similar methodology

Example 15 Implementation of the Extended Supermotif to Improve theBinding Capacity of Native Epitopes by Creating Analogs

HLA motifs and supermotifs (comprising primary and/or secondaryresidues) are useful in the identification and preparation of highlycross-reactive native peptides, as demonstrated herein. Moreover, thedefinition of HLA motifs and supermotifs also allows one to engineerhighly cross-reactive epitopes by identifying residues within a nativepeptide sequence which can be analoged to confer upon the peptidecertain characteristics, e.g. greater cross-reactivity within the groupof HLA molecules that comprise a supertype, and/or greater bindingaffinity for some or all of those HLA molecules. Examples of analogingpeptides to exhibit modulated binding affinity are set forth in thisexample.

Analoging at Primary Anchor Residues

Peptide engineering strategies are implemented to further increase thecross-reactivity of the epitopes. For example, the main anchors ofA2-supermotif-bearing peptides are altered, for example, to introduce apreferred L, I, V, or M at position 2, and I or V at the C-terminus.

To analyze the cross-reactivity of the analog peptides, each engineeredanalog is initially tested for binding to the prototype A2 supertypeallele A*0201, then, if A*0201 binding capacity is maintained, forA2-supertype cross-reactivity.

Alternatively, a peptide is confirmed as binding one or all supertypemembers and then analoged to modulate binding affinity to any one (ormore) of the supertype members to add population coverage.

The selection of analogs for immunogenicity in a cellular screeninganalysis is typically further restricted by the capacity of the parentwild type (WT) peptide to bind at least weakly, i.e., bind at an IC₅₀ of5000 nM or less, to three of more A2 supertype alleles. The rationalefor this requirement is that the WT peptides must be presentendogenously in sufficient quantity to be biologically relevant.Analoged peptides have been shown to have increased immunogenicity andcross-reactivity by T cells specific for the parent epitope (see, e.g.,Parkhurst et al., J. Immunol. 157:2539, 1996; and Pogue et al., Proc.Natl. Acad. Sci. USA 92:8166, 1995).

In the cellular screening of these peptide analogs, it is important toconfirm that analog-specific CTLs are also able to recognize thewild-type peptide and, when possible, target cells that endogenouslyexpress the epitope.

Analoging of HLA-A3 and B7-Supermotif-Bearing Peptides

Analogs of HLA-A3 supermotif-bearing epitopes are generated usingstrategies similar to those employed in analoging HLA-A2supermotif-bearing peptides. For example, peptides binding to 3/5 of theA3-supertype molecules are engineered at primary anchor residues topossess a preferred residue (V, S, M, or A) at position 2.

The analog peptides are then tested for the ability to bind A*03 andA*11 (prototype A3 supertype alleles). Those peptides that demonstrate≦500 nM binding capacity are then confirmed as having A3-supertypecross-reactivity.

Similarly to the A2- and A3-motif bearing peptides, peptides binding 3or more B7-supertype alleles can be improved, where possible, to achieveincreased cross-reactive binding or greater binding affinity or bindinghalf life. B7 supermotif-bearing peptides are, for example, engineeredto possess a preferred residue (V, I, L, or F) at the C-terminal primaryanchor position, as demonstrated by Sidney et al. (J. Immunol.157:3480-3490, 1996).

Analoging at primary anchor residues of other motif and/orsupermotif-bearing epitopes is performed in a like manner.

The analog peptides are then be confirmed for immunogenicity, typicallyin a cellular screening assay. Again, it is generally important todemonstrate that analog-specific CTLs are also able to recognize thewild-type peptide and, when possible, targets that endogenously expressthe epitope.

Analoging at Secondary Anchor Residues

Moreover, HLA supermotifs are of value in engineering highlycross-reactive peptides and/or peptides that bind HLA molecules withincreased affinity by identifying particular residues at secondaryanchor positions that are associated with such properties. For example,the binding capacity of a B7 supermotif-bearing peptide with an Fresidue at position 1 is analyzed. The peptide is then analoged to, forexample, substitute L for F at position 1. The analoged peptide isevaluated for increased binding affinity, binding half life and/orincreased cross-reactivity. Such a procedure identifies analogedpeptides with enhanced properties.

Engineered analogs with sufficiently improved binding capacity orcross-reactivity can also be tested for immunogenicity inHLA-B7-transgenic mice, following for example, IFA immunization orlipopeptide immunization. Analoged peptides are additionally tested forthe ability to stimulate a recall response using PBMC from patients with238P1B2-expressing tumors.

Other Analoging Strategies

Another form of peptide analoging, unrelated to anchor positions,involves the substitution of a cysteine with α-amino butyric acid. Dueto its chemical nature, cysteine has the propensity to form disulfidebridges and sufficiently alter the peptide structurally so as to reducebinding capacity. Substitution of α-amino butyric acid for cysteine notonly alleviates this problem, but has been shown to improve binding andcrossbinding capabilities in some instances (see, e.g., the review bySette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I.Chen, John Wiley & Sons, England, 1999).

Thus, by the use of single amino acid substitutions, the bindingproperties and/or cross-reactivity of peptide ligands for HLA supertypemolecules can be modulated.

Example 16 Identification and Confirmation of 238P1B2-Derived Sequenceswith HLA-DR Binding Motifs

Peptide epitopes bearing an HLA class II supermotif or motif areidentified and confirmed as outlined below using methodology similar tothat described for HLA Class I peptides.

Selection of HLA-DR-Supermotif-Bearing Epitopes.

To identify 238P1B2-derived, HLA class II HTL epitopes, a 238P1B2antigen is analyzed for the presence of sequences bearing anHLA-DR-motif or supermotif. Specifically, 15-mer sequences are selectedcomprising a DR-supermotif, comprising a 9-mer core, and three-residueN- and C-terminal flanking regions (15 amino acids total).

Protocols for predicting peptide binding to DR molecules have beendeveloped (Southwood et al., J. Immunol. 160:3363-3373, 1998). Theseprotocols, specific for individual DR molecules, allow the scoring, andranking, of 9-mer core regions. Each protocol not only scores peptidesequences for the presence of DR-supermotif primary anchors (i.e., atposition 1 and position 6) within a 9-mer core, but additionallyevaluates sequences for the presence of secondary anchors. Usingallele-specific selection tables (see, e.g., Southwood et al., ibid.),it has been found that these protocols efficiently select peptidesequences with a high probability of binding a particular DR molecule.Additionally, it has been found that performing these protocols intandem, specifically those for DR1, DR4w4, and DR7, can efficientlyselect DR cross-reactive peptides.

The 238P1B2-derived peptides identified above are tested for theirbinding capacity for various common HLA-DR molecules. All peptides areinitially tested for binding to the DR molecules in the primary panel:DR1, DR4w4, and DR7. Peptides binding at least two of these three DRmolecules are then tested for binding to DR2w2 β1, DR2w2 β2, DR6w19, andDR9 molecules in secondary assays. Finally, peptides binding at leasttwo of the four secondary panel DR molecules, and thus cumulatively atleast four of seven different DR molecules, are screened for binding toDR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides bindingat least seven of the ten DR molecules comprising the primary,secondary, and tertiary screening assays are considered cross-reactiveDR binders. 238P1B2-derived peptides found to bind common HLA-DR allelesare of particular interest.

Selection of DR3 Motif Peptides

Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, andHispanic populations, DR3 binding capacity is a relevant criterion inthe selection of HTL epitopes. Thus, peptides shown to be candidates mayalso be assayed for their DR3 binding capacity. However, in view of thebinding specificity of the DR3 motif, peptides binding only to DR3 canalso be considered as candidates for inclusion in a vaccine formulation.

To efficiently identify peptides that bind DR3, target 238P1B2 antigensare analyzed for sequences carrying one of the two DR3-specific bindingmotifs reported by Geluk et al. (J. Immunol. 152:5742-5748, 1994). Thecorresponding peptides are then synthesized and confirmed as having theability to bind DR3 with an affinity of 1 μM or better, i.e., less than1 μM. Peptides are found that meet this binding criterion and qualify asHLA class II high affinity binders.

DR3 binding epitopes identified in this manner are included in vaccinecompositions with DR supermotif-bearing peptide epitopes.

Similarly to the case of HLA class I motif-bearing peptides, the classII motif-bearing peptides are analoged to improve affinity orcross-reactivity. For example, aspartic acid at position 4 of the 9-mercore sequence is an optimal residue for DR3 binding, and substitutionfor that residue often improves DR 3 binding.

Example 17 Immunogenicity of 238P1B2-Derived HTL Epitopes

This example determines immunogenic DR supermotif- and DR3 motif-bearingepitopes among those identified using the methodology set forth herein.

Immunogenicity of HTL epitopes are confirmed in a manner analogous tothe determination of immunogenicity of CTL epitopes, by assessing theability to stimulate HTL responses and/or by using appropriatetransgenic mouse models. Immunogenicity is determined by screening for:1.) in vitro primary induction using normal PBMC or 2.) recall responsesfrom patients who have 238P1B2-expressing tumors.

Example 18 Calculation of Phenotypic Frequencies of HLA-Supertypes inVarious Ethnic Backgrounds to Determine Breadth of Population Coverage

This example illustrates the assessment of the breadth of populationcoverage of a vaccine composition comprised of multiple epitopescomprising multiple supermotifs and/or motifs.

In order to analyze population coverage, gene frequencies of HLA allelesare determined. Gene frequencies for each HLA allele are calculated fromantigen or allele frequencies utilizing the binomial distributionformulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., Human Immunol.45:79-93, 1996). To obtain overall phenotypic frequencies, cumulativegene frequencies are calculated, and the cumulative antigen frequenciesderived by the use of the inverse formula [af=1−(1−Cgf)²].

Where frequency data is not available at the level of DNA typing,correspondence to the serologically defined antigen frequencies isassumed. To obtain total potential supertype population coverage nolinkage disequilibrium is assumed, and only alleles confirmed to belongto each of the supertypes are included (minimal estimates). Estimates oftotal potential coverage achieved by inter-loci combinations are made byadding to the A coverage the proportion of the non-A covered populationthat could be expected to be covered by the B alleles considered (e.g.,total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3,A11, A31, A*3301, and A*6801. Although the A3-like supertype may alsoinclude A34, A66, and A*7401, these alleles were not included in overallfrequency calculations. Likewise, confirmed members of the A2-likesupertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206,A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmedalleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601,B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, andB*5602).

Population coverage achieved by combining the A2-, A3- and B7-supertypesis approximately 86% in five major ethnic groups. Coverage may beextended by including peptides bearing the A1 and A24 motifs. Onaverage, A1 is present in 12% and A24 in 29% of the population acrossfive different major ethnic groups (Caucasian, North American Black,Chinese, Japanese, and Hispanic). Together, these alleles arerepresented with an average frequency of 39% in these same ethnicpopulations. The total coverage across the major ethnicities when A1 andA24 are combined with the coverage of the A2-, A3- and B7-supertypealleles is >95%. An analogous approach can be used to estimatepopulation coverage achieved with combinations of class II motif-bearingepitopes.

Immunogenicity studies in humans (e.g., Bertoni et al., J. Clin. Invest.100:503, 1997; Doolan et al., Immunity 7:97, 1997; and Threlkeld et al.,J. Immunol. 159:1648, 1997) have shown that highly cross-reactivebinding peptides are almost always recognized as epitopes. The use ofhighly cross-reactive binding peptides is an important selectioncriterion in identifying candidate epitopes for inclusion in a vaccinethat is immunogenic in a diverse population.

With a sufficient number of epitopes (as disclosed herein and from theart), an average population coverage is predicted to be greater than 95%in each of five major ethnic populations. The game theory Monte Carlosimulation analysis, which is known in the art (see e.g., Osborne, M. J.and Rubinstein, A. “A course in game theory” MIT Press, 1994), can beused to estimate what percentage of the individuals in a populationcomprised of the Caucasian, North American Black, Japanese, Chinese, andHispanic ethnic groups would recognize the vaccine epitopes describedherein. A preferred percentage is 90%. A more preferred percentage is95%.

Example 19 CTL Recognition of Endogenously Processed Antigens afterPriming

This example confirms that CTL induced by native or analoged peptideepitopes identified and selected as described herein recognizeendogenously synthesized, i.e., native antigens.

Effector cells isolated from transgenic mice that are immunized withpeptide epitopes, for example HLA-A2 supermotif-bearing epitopes, arere-stimulated in vitro using peptide-coated stimulator cells. Six dayslater, effector cells are assayed for cytotoxicity and the cell linesthat contain peptide-specific cytotoxic activity are furtherre-stimulated. An additional six days later, these cell lines are testedfor cytotoxic activity on ⁵¹Cr labeled Jurkat-A2.1/K^(b) target cells inthe absence or presence of peptide, and also tested on ⁵¹Cr labeledtarget cells bearing the endogenously synthesized antigen, i.e. cellsthat are stably transfected with 238P1B2 expression vectors.

The results demonstrate that CTL lines obtained from animals primed withpeptide epitope recognize endogenously synthesized 238P1B2 antigen. Thechoice of transgenic mouse model to be used for such an analysis dependsupon the epitope(s) that are being evaluated. In addition toHLA-A*0201/K^(b) transgenic mice, several other transgenic mouse modelsincluding mice with human A11, which may also be used to evaluate A3epitopes, and B7 alleles have been characterized and others (e.g.,transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 andHLA-DR3 mouse models have also been developed, which may be used toevaluate HTL epitopes.

Example 20 Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice

This example illustrates the induction of CTLs and HTLs in transgenicmice, by use of a 238P1B2-derived CTL and HTL peptide vaccinecompositions. The vaccine composition used herein comprise peptides tobe administered to a patient with a 238P1B2-expressing tumor. Thepeptide composition can comprise multiple CTL and/or HTL epitopes. Theepitopes are identified using methodology as described herein. Thisexample also illustrates that enhanced immunogenicity can be achieved byinclusion of one or more HTL epitopes in a CTL vaccine composition; sucha peptide composition can comprise an HTL epitope conjugated to a CTLepitope. The CTL epitope can be one that binds to multiple HLA familymembers at an affinity of 500 nM or less, or analogs of that epitope.The peptides may be lipidated, if desired.

Immunization procedures: Immunization of transgenic mice is performed asdescribed (Alexander et al., J. Immunol. 159:4753-4761, 1997). Forexample, A2/K^(b) mice, which are transgenic for the human HLA A2.1allele and are used to confirm the immunogenicity of HLA-A*0201 motif-or HLA-A2 supermotif-bearing epitopes, and are primed subcutaneously(base of the tail) with a 0.1 ml of peptide in Incomplete Freund'sAdjuvant, or if the peptide composition is a lipidated CTL/HTLconjugate, in DMSO/saline, or if the peptide composition is apolypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days afterpriming, splenocytes obtained from these animals are restimulated withsyngenic irradiated LPS-activated lymphoblasts coated with peptide.

Cell lines: Target cells for peptide-specific cytotoxicity assays areJurkat cells transfected with the HLA-A2.1/K^(b) chimeric gene (e.g.,Vitiello et al., J. Exp. Med. 173:1007, 1991)

In vitro CTL activation: One week after priming, spleen cells (30×10⁶cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000rads), peptide coated lymphoblasts (10×10⁶ cells/flask) in 10 ml ofculture medium/T25 flask. After six days, effector cells are harvestedand assayed for cytotoxic activity.

Assay for cytotoxic activity: Target cells (1.0 to 1.5×10⁶) areincubated at 37° C. in the presence of 200 μl of ⁵¹Cr. After 60 minutes,cells are washed three times and resuspended in R10 medium. Peptide isadded where required at a concentration of 1 μg/ml. For the assay, 10⁴⁵¹Cr-labeled target cells are added to different concentrations ofeffector cells (final volume of 200 μl) in U-bottom 96-well plates.After a six hour incubation period at 37° C., a 0.1 ml aliquot ofsupernatant is removed from each well and radioactivity is determined ina Micromedic automatic gamma counter. The percent specific lysis isdetermined by the formula: percent specific release=100×(experimentalrelease−spontaneous release)/(maximum release−spontaneous release). Tofacilitate comparison between separate CTL assays run under the sameconditions, % ⁵¹Cr release data is expressed as lytic units/10⁶ cells.One lytic unit is arbitrarily defined as the number of effector cellsrequired to achieve 30% lysis of 10,000 target cells in a six hour ⁵¹Crrelease assay. To obtain specific lytic units/10⁶, the lytic units/10⁶obtained in the absence of peptide is subtracted from the lyticunits/10⁶ obtained in the presence of peptide. For example, if 30% ⁵¹Crrelease is obtained at the effector (E): target (T) ratio of 50:1 (i.e.,5×10⁵ effector cells for 10,000 targets) in the absence of peptide and5:1 (i.e., 5×10⁴ effector cells for 10,000 targets) in the presence ofpeptide, the specific lytic units would be:[(1/50,000)−(1/500,000)]×10⁶⁼¹⁸ LU.

The results are analyzed to assess the magnitude of the CTL responses ofanimals injected with the immunogenic CTL/HTL conjugate vaccinepreparation and are compared to the magnitude of the CTL responseachieved using, for example, CTL epitopes as outlined above in theExample entitled “Confirmation of Immunogenicity”. Analyses similar tothis may be performed to confirm the immunogenicity of peptideconjugates containing multiple CTL epitopes and/or multiple HTLepitopes. In accordance with these procedures, it is found that a CTLresponse is induced, and concomitantly that an HTL response is inducedupon administration of such compositions.

Example 21 Selection of CTL and HTL Epitopes for Inclusion in an238P1B2-Specific Vaccine

This example illustrates a procedure for selecting peptide epitopes forvaccine compositions of the invention. The peptides in the compositioncan be in the form of a nucleic acid sequence, either single or one ormore sequences (i.e., minigene) that encodes peptide(s), or can besingle and/or polyepitopic peptides.

The following principles are utilized when selecting a plurality ofepitopes for inclusion in a vaccine composition. Each of the followingprinciples is balanced in order to make the selection.

Epitopes are selected which, upon administration, mimic immune responsesthat are correlated with 238P1B2 clearance. The number of epitopes useddepends on observations of patients who spontaneously clear 238P1B2. Forexample, if it has been observed that patients who spontaneously clear238P1B2 generate an immune response to at least three (3) from 238P1B2antigen, then three or four (3-4) epitopes should be included for HLAclass I. A similar rationale is used to determine HLA class II epitopes.

Epitopes are often selected that have a binding affinity of an IC₅₀ of500 nM or less for an HLA class I molecule, or for class II, an IC₅₀ of1000 nM or less; or HLA Class I peptides with high binding scores fromthe BIMAS web site.

In order to achieve broad coverage of the vaccine through out a diversepopulation, sufficient supermotif bearing peptides, or a sufficientarray of allele-specific motif bearing peptides, are selected to givebroad population coverage. In one embodiment, epitopes are selected toprovide at least 80% population coverage. A Monte Carlo analysis, astatistical evaluation known in the art, can be employed to assessbreadth, or redundancy, of population coverage.

When creating polyepitopic compositions, or a minigene that encodessame, it is typically desirable to generate the smallest peptidepossible that encompasses the epitopes of interest. The principlesemployed are similar, if not the same, as those employed when selectinga peptide comprising nested epitopes. For example, a protein sequencefor the vaccine composition is selected because it has maximal number ofepitopes contained within the sequence, i.e., it has a highconcentration of epitopes. Epitopes may be nested or overlapping (i.e.,frame shifted relative to one another). For example, with overlappingepitopes, two 9-mer epitopes and one 10-mer epitope can be present in a10 amino acid peptide. Each epitope can be exposed and bound by an HLAmolecule upon administration of such a peptide. A multi-epitopic,peptide can be generated synthetically, recombinantly, or via cleavagefrom the native source. Alternatively, an analog can be made of thisnative sequence, whereby one or more of the epitopes comprisesubstitutions that alter the cross-reactivity and/or binding affinityproperties of the polyepitopic peptide. Such a vaccine composition isadministered for therapeutic or prophylactic purposes. This embodimentprovides for the possibility that an as yet undiscovered aspect ofimmune system processing will apply to the native nested sequence andthereby facilitate the production of therapeutic or prophylactic immuneresponse-inducing vaccine compositions. Additionally such an embodimentprovides for the possibility of motif-bearing epitopes for an HLA makeupthat is presently unknown. Furthermore, this embodiment (absent thecreating of any analogs) directs the immune response to multiple peptidesequences that are actually present in 238P1B2, thus avoiding the needto evaluate any junctional epitopes. Lastly, the embodiment provides aneconomy of scale when producing nucleic acid vaccine compositions.Related to this embodiment, computer programs can be derived inaccordance with principles in the art, which identify in a targetsequence, the greatest number of epitopes per sequence length.

A vaccine composition comprised of selected peptides, when administered,is safe, efficacious, and elicits an immune response similar inmagnitude to an immune response that controls or clears cells that bearor overexpress 238P1B2.

Example 22 Construction of “Minigene” Multi-Epitope DNA Plasmids

This example discusses the construction of a minigene expressionplasmid. Minigene plasmids may, of course, contain variousconfigurations of B cell, CTL and/or HTL epitopes or epitope analogs asdescribed herein.

A minigene expression plasmid typically includes multiple CTL and HTLpeptide epitopes. In the present example, HLA-A2, -A3, -B7supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearingpeptide epitopes are used in conjunction with DR supermotif-bearingepitopes and/or DR3 epitopes. HLA class I supermotif or motif-bearingpeptide epitopes derived 238P1B2, are selected such that multiplesupermotifs/motifs are represented to ensure broad population coverage.Similarly, HLA class II epitopes are selected from 238P1B2 to providebroad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearingepitopes and HLA DR-3 motif-bearing epitopes are selected for inclusionin the minigene construct. The selected CTL and HTL epitopes are thenincorporated into a minigene for expression in an expression vector.

Such a construct may additionally include sequences that direct the HTLepitopes to the endoplasmic reticulum. For example, the Ii protein maybe fused to one or more HTL epitopes as described in the art, whereinthe CLIP sequence of the Ii protein is removed and replaced with an HLAclass II epitope sequence so that HLA class II epitope is directed tothe endoplasmic reticulum, where the epitope binds to an HLA class IImolecules.

This example illustrates the methods to be used for construction of aminigene-bearing expression plasmid. Other expression vectors that maybe used for minigene compositions are available and known to those ofskill in the art.

The minigene DNA plasmid of this example contains a consensus Kozaksequence and a consensus murine kappa Ig-light chain signal sequencefollowed by CTL and/or HTL epitopes selected in accordance withprinciples disclosed herein. The sequence encodes an open reading framefused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1Myc-His vector.

Overlapping oligonucleotides that can, for example, average about 70nucleotides in length with 15 nucleotide overlaps, are synthesized andHPLC-purified. The oligonucleotides encode the selected peptide epitopesas well as appropriate linker nucleotides, Kozak sequence, and signalsequence. The final multiepitope minigene is assembled by extending theoverlapping oligonucleotides in three sets of reactions using PCR. APerkin/Elmer 9600 PCR machine is used and a total of 30 cycles areperformed using the following conditions: 95° C. for 15 sec, annealingtemperature (5° below the lowest calculated Tm of each primer pair) for30 sec, and 72° C. for 1 min.

For example, a minigene is prepared as follows. For a first PCRreaction, 5 μg of each of two oligonucleotides are annealed andextended: In an example using eight oligonucleotides, i.e., four pairsof primers, oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM(NH4)₂SO₄, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO₄, 0.1% Triton X-100,100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. Thefull-length dimer products are gel-purified, and two reactionscontaining the product of 1+2 and 3+4, and the product of 5+6 and 7+8are mixed, annealed, and extended for 10 cycles. Half of the tworeactions are then mixed, and 5 cycles of annealing and extensioncarried out before flanking primers are added to amplify the full lengthproduct. The full-length product is gel-purified and cloned intopCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 23 The Plasmid Construct and the Degree to which it InducesImmunogenicity

The degree to which a plasmid construct, for example a plasmidconstructed in accordance with the previous Example, is able to induceimmunogenicity is confirmed in vitro by determining epitope presentationby APC following transduction or transfection of the APC with anepitope-expressing nucleic acid construct. Such a study determines“antigenicity” and allows the use of human APC. The assay determines theability of the epitope to be presented by the APC in a context that isrecognized by a T cell by quantifying the density of epitope-HLA class Icomplexes on the cell surface. Quantitation can be performed by directlymeasuring the amount of peptide eluted from the APC (see, e.g., Sijts etal., J. Immunol. 156:683-692, 1996; Demotz et al., Nature 342:682-684,1989); or the number of peptide-HLA class I complexes can be estimatedby measuring the amount of lysis or lymphokine release induced bydiseased or transfected target cells, and then determining theconcentration of peptide necessary to obtain equivalent levels of lysisor lymphokine release (see, e.g., Kageyama et al., J. Immunol.154:567-576, 1995).

Alternatively, immunogenicity is confirmed through in vivo injectionsinto mice and subsequent in vitro assessment of CTL and HTL activity,which are analyzed using cytotoxicity and proliferation assays,respectively, as detailed e.g., in Alexander et al., Immunity 1:751-761,1994.

For example, to confirm the capacity of a DNA minigene constructcontaining at least one HLA-A2 supermotif peptide to induce CTLs invivo, HLA-A2.1I/K^(b) transgenic mice, for example, are immunizedintramuscularly with 100 μg of naked cDNA. As a means of comparing thelevel of CTLs induced by cDNA immunization, a control group of animalsis also immunized with an actual peptide composition that comprisesmultiple epitopes synthesized as a single polypeptide as they would beencoded by the minigene.

Splenocytes from immunized animals are stimulated twice with each of therespective compositions (peptide epitopes encoded in the minigene or thepolyepitopic peptide), then assayed for peptide-specific cytotoxicactivity in a ⁵¹Cr release assay. The results indicate the magnitude ofthe CTL response directed against the A2-restricted epitope, thusindicating the in vivo immunogenicity of the minigene vaccine andpolyepitopic vaccine.

It is, therefore, found that the minigene elicits immune responsesdirected toward the HLA-A2 supermotif peptide epitopes as does thepolyepitopic peptide vaccine. A similar analysis is also performed usingother HLA-A3 and HLA-B7 transgenic mouse models to assess CTL inductionby HLA-A3 and HLA-B7 motif or supermotif epitopes, whereby it is alsofound that the minigene elicits appropriate immune responses directedtoward the provided epitopes.

To confirm the capacity of a class II epitope-encoding minigene toinduce HTLs in vivo, DR transgenic mice, or for those epitopes thatcross react with the appropriate mouse MHC molecule, I-A^(b)-restrictedmice, for example, are immunized intramuscularly with 100 μg of plasmidDNA. As a means of comparing the level of HTLs induced by DNAimmunization, a group of control animals is also immunized with anactual peptide composition emulsified in complete Freund's adjuvant.CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunizedanimals and stimulated with each of the respective compositions(peptides encoded in the minigene). The HTL response is measured using a³H-thymidine incorporation proliferation assay, (see, e.g., Alexander etal. Immunity 1:751-761, 1994). The results indicate the magnitude of theHTL response, thus demonstrating the in vivo immunogenicity of theminigene.

DNA minigenes, constructed as described in the previous Example, canalso be confirmed as a vaccine in combination with a boosting agentusing a prime boost protocol. The boosting agent can consist ofrecombinant protein (e.g., Barnett et al., Aids Res. and HumanRetroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia,for example, expressing a minigene or DNA encoding the complete proteinof interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegahet al., Proc. Natl. Acad. Sci. USA 95:7648-53, 1998; Hanke andMcMichael, Immunol. Letters 66:177-181, 1999; and Robinson et al.,Nature Med. 5:526-34, 1999).

For example, the efficacy of the DNA minigene used in a prime boostprotocol is initially evaluated in transgenic mice. In this example,A2.1/K^(b) transgenic mice are immunized IM with 100 μg of a DNAminigene encoding the immunogenic peptides including at least one HLA-A2supermotif-bearing peptide. After an incubation period (ranging from 3-9weeks), the mice are boosted IP with 10⁷ pfu/mouse of a recombinantvaccinia virus expressing the same sequence encoded by the DNA minigene.Control mice are immunized with 100 μg of DNA or recombinant vacciniawithout the minigene sequence, or with DNA encoding the minigene, butwithout the vaccinia boost. After an additional incubation period of twoweeks, splenocytes from the mice are immediately assayed forpeptide-specific activity in an ELISPOT assay. Additionally, splenocytesare stimulated in vitro with the A2-restricted peptide epitopes encodedin the minigene and recombinant vaccinia, then assayed forpeptide-specific activity in an alpha, beta and/or gamma IFN ELISA.

It is found that the minigene utilized in a prime-boost protocol elicitsgreater immune responses toward the HLA-A2 supermotif peptides than withDNA alone. Such an analysis can also be performed using HLA-A11 orHLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 orHLA-B7 motif or supermotif epitopes. The use of prime boost protocols inhumans is described below in the Example entitled “Induction of CTLResponses Using a Prime Boost Protocol.”

Example 24 Peptide Compositions for Prophylactic Uses

Vaccine compositions of the present invention can be used to prevent238P1B2 expression in persons who are at risk for tumors that bear thisantigen. For example, a polyepitopic peptide epitope composition (or anucleic acid comprising the same) containing multiple CTL and HTLepitopes such as those selected in the above Examples, which are alsoselected to target greater than 80% of the population, is administeredto individuals at risk for a 238P1B2-associated tumor.

For example, a peptide-based composition is provided as a singlepolypeptide that encompasses multiple epitopes. The vaccine is typicallyadministered in a physiological solution that comprises an adjuvant,such as Incomplete Freunds Adjuvant. The dose of peptide for the initialimmunization is from about 1 to about 50,000 μg, generally 100-5,000 μg,for a 70 kg patient. The initial administration of vaccine is followedby booster dosages at 4 weeks followed by evaluation of the magnitude ofthe immune response in the patient, by techniques that determine thepresence of epitope-specific CTL populations in a PBMC sample.Additional booster doses are administered as required. The compositionis found to be both safe and efficacious as a prophylaxis against238P1B2-associated disease.

Alternatively, a composition typically comprising transfecting agents isused for the administration of a nucleic acid-based vaccine inaccordance with methodologies known in the art and disclosed herein.

Example 25 Polyepitopic Vaccine Compositions Derived from Native 238P1B2Sequences

A native 238P1B2 polyprotein sequence is analyzed, preferably usingcomputer algorithms defined for each class I and/or class II supermotifor motif, to identify “relatively short” regions of the polyprotein thatcomprise multiple epitopes. The “relatively short” regions arepreferably less in length than an entire native antigen. This relativelyshort sequence that contains multiple distinct or overlapping, “nested”epitopes is selected; it can be used to generate a minigene construct.The construct is engineered to express the peptide, which corresponds tothe native protein sequence. The “relatively short” peptide is generallyless than 250 amino acids in length, often less than 100 amino acids inlength, preferably less than 75 amino acids in length, and morepreferably less than 50 amino acids in length. The protein sequence ofthe vaccine composition is selected because it has maximal number ofepitopes contained within the sequence, i.e., it has a highconcentration of epitopes. As noted herein, epitope motifs may be nestedor overlapping (i.e., frame shifted relative to one another). Forexample, with overlapping epitopes, two 9-mer epitopes and one 10-merepitope can be present in a 10 amino acid peptide. Such a vaccinecomposition is administered for therapeutic or prophylactic purposes.

The vaccine composition will include, for example, multiple CTL epitopesfrom 238P1B2 antigen and at least one HTL epitope. This polyepitopicnative sequence is administered either as a peptide or as a nucleic acidsequence which encodes the peptide. Alternatively, an analog can be madeof this native sequence, whereby one or more of the epitopes comprisesubstitutions that alter the cross-reactivity and/or binding affinityproperties of the polyepitopic peptide.

The embodiment of this example provides for the possibility that an asyet undiscovered aspect of immune system processing will apply to thenative nested sequence and thereby facilitate the production oftherapeutic or prophylactic immune response-inducing vaccinecompositions. Additionally such an embodiment provides for thepossibility of motif-bearing epitopes for an HLA makeup that ispresently unknown. Furthermore, this embodiment (excluding an analogedembodiment) directs the immune response to multiple peptide sequencesthat are actually present in native 238P1B2, thus avoiding the need toevaluate any junctional epitopes. Lastly, the embodiment provides aneconomy of scale when producing peptide or nucleic acid vaccinecompositions.

Related to this embodiment, computer programs are available in the artwhich can be used to identify in a target sequence, the greatest numberof epitopes per sequence length.

Example 26 Polyepitopic Vaccine Compositions from Multiple Antigens

The 238P1B2 peptide epitopes of the present invention are used inconjunction with epitopes from other target tumor-associated antigens,to create a vaccine composition that is useful for the prevention ortreatment of cancer that expresses 238P1B2 and such other antigens. Forexample, a vaccine composition can be provided as a single polypeptidethat incorporates multiple epitopes from 238P1B2 as well astumor-associated antigens that are often expressed with a target cancerassociated with 238P1B2 expression, or can be administered as acomposition comprising a cocktail of one or more discrete epitopes.Alternatively, the vaccine can be administered as a minigene constructor as dendritic cells which have been loaded with the peptide epitopesin vitro.

Example 27 Use of Peptides to Evaluate an Immune Response

Peptides of the invention may be used to analyze an immune response forthe presence of specific antibodies, CTL or HTL directed to 238P1B2.Such an analysis can be performed in a manner described by Ogg et al.,Science 279:2103-2106, 1998. In this Example, peptides in accordancewith the invention are used as a reagent for diagnostic or prognosticpurposes, not as an immunogen.

In this example highly sensitive human leukocyte antigen tetramericcomplexes (“tetramers”) are used for a cross-sectional analysis of, forexample, 238P1B2 HLA-A*0201-specific CTL frequencies from HLAA*0201-positive individuals at different stages of disease or followingimmunization comprising an 238P1B2 peptide containing an A*0201 motif.Tetrameric complexes are synthesized as described (Musey et al., N.Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201in this example) and β2-microglobulin are synthesized by means of aprokaryotic expression system. The heavy chain is modified by deletionof the transmembrane-cytosolic tail and COOH-terminal addition of asequence containing a BirA enzymatic biotinylation site. The heavychain, β2-microglobulin, and peptide are refolded by dilution. The 45-kDrefolded product is isolated by fast protein liquid chromatography andthen biotinylated by BirA in the presence of biotin (Sigma, St. Louis,Mo.), adenosine 5′ triphosphate and magnesium.Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, andthe tetrameric product is concentrated to 1 mg/ml. The resulting productis referred to as tetramer-phycoerythrin.

For the analysis of patient blood samples, approximately one millionPBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl ofcold phosphate-buffered saline. Tri-color analysis is performed with thetetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. ThePBMCs are incubated with tetramer and antibodies on ice for 30 to 60 minand then washed twice before formaldehyde fixation. Gates are applied tocontain >99.98% of control samples. Controls for the tetramers includeboth A*0201-negative individuals and A*0201-positive non-diseaseddonors. The percentage of cells stained with the tetramer is thendetermined by flow cytometry. The results indicate the number of cellsin the PBMC sample that contain epitope-restricted CTLs, thereby readilyindicating the extent of immune response to the 238P1B2 epitope, andthus the status of exposure to 238P1B2, or exposure to a vaccine thatelicits a protective or therapeutic response.

Example 28 Use of Peptide Epitopes to Evaluate Recall Responses

The peptide epitopes of the invention are used as reagents to evaluate Tcell responses, such as acute or recall responses, in patients. Such ananalysis may be performed on patients who have recovered from238P1B2-associated disease or who have been vaccinated with an 238P1B2vaccine.

For example, the class I restricted CTL response of persons who havebeen vaccinated may be analyzed. The vaccine may be any 238P1B2 vaccine.PBMC are collected from vaccinated individuals and HLA typed.Appropriate peptide epitopes of the invention that, optimally, bearsupermotifs to provide cross-reactivity with multiple HLA supertypefamily members, are then used for analysis of samples derived fromindividuals who bear that HLA type.

PBMC from vaccinated individuals are separated on Ficoll-Histopaquedensity gradients (Sigma Chemical Co., St. Louis, Mo.), washed threetimes in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCOLaboratories) supplemented with L-glutamine (2 mM), penicillin (50U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10%heat-inactivated human AB serum (complete RPMI) and plated usingmicroculture formats. A synthetic peptide comprising an epitope of theinvention is added at 10 μg/ml to each well and HBV core 128-140 epitopeis added at 1 μg/ml to each well as a source of T cell help during thefirst week of stimulation.

In the microculture format, 4×10⁵ PBMC are stimulated with peptide in 8replicate cultures in 96-well round bottom plate in 100 μl/well ofcomplete RPMI. On days 3 and 10, 100 μl of complete RPMI and 20 U/mlfinal concentration of rIL-2 are added to each well. On day 7 thecultures are transferred into a 96-well flat-bottom plate andrestimulated with peptide, rIL-2 and 10⁵ irradiated (3,000 rad)autologous feeder cells. The cultures are tested for cytotoxic activityon day 14. A positive CTL response requires two or more of the eightreplicate cultures to display greater than 10% specific ⁵¹Cr release,based on comparison with non-diseased control subjects as previouslydescribed (Rehermann, et al., Nature Med. 2:1104, 1108, 1996; Rehermannet al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J.Clin. Invest. 98:1432-1440, 1996).

Target cell lines are autologous and allogeneic EBV-transformed B-LCLthat are either purchased from the American Society forHistocompatibility and Immunogenetics (ASHI, Boston, Mass.) orestablished from the pool of patients as described (Guilhot, et al. J.Virol. 66:2670-2678, 1992).

Cytotoxicity assays are performed in the following manner. Target cellsconsist of either allogeneic HLA-matched or autologous EBV-transformed Blymphoblastoid cell line that are incubated overnight with the syntheticpeptide epitope of the invention at 10 μM, and labeled with 100 μCi of⁵¹Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after whichthey are washed four times with HBSS.

Cytolytic activity is determined in a standard 4-h, split well ⁵¹Crrelease assay using U-bottomed 96 well plates containing 3,000targets/well. Stimulated PBMC are tested at effector/target (E/T) ratiosof 20-50:1 on day 14. Percent cytotoxicity is determined from theformula: 100×[(experimental release-spontaneous release)/maximumrelease-spontaneous release)]. Maximum release is determined by lysis oftargets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis,Mo.). Spontaneous release is <25% of maximum release for allexperiments.

The results of such an analysis indicate the extent to whichHLA-restricted CTL populations have been stimulated by previous exposureto 238P1B2 or an 238P1B2 vaccine.

Similarly, Class II restricted HTL responses may also be analyzed.Purified PBMC are cultured in a 96-well flat bottom plate at a densityof 1.5×10⁵ cells/well and are stimulated with 10 μg/ml synthetic peptideof the invention, whole 238P1B2 antigen, or PHA. Cells are routinelyplated in replicates of 4-6 wells for each condition. After seven daysof culture, the medium is removed and replaced with fresh mediumcontaining 10 U/ml IL-2. Two days later, 1 μCi ³H-thymidine is added toeach well and incubation is continued for an additional 18 hours.Cellular DNA is then harvested on glass fiber mats and analyzed for³H-thymidine incorporation. Antigen-specific T cell proliferation iscalculated as the ratio of ³H-thymidine incorporation in the presence ofantigen divided by the ³H-thymidine incorporation in the absence ofantigen.

Example 29 Induction of Specific CTL Response in Humans

A human clinical trial for an immunogenic composition comprising CTL andHTL epitopes of the invention is set up as an IND Phase I, doseescalation study and carried out as a randomized, double-blind,placebo-controlled trial. Such a trial is designed, for example, asfollows:

A total of about 27 individuals are enrolled and divided into 3 groups:

Group I: 3 subjects are injected with placebo and 6 subjects areinjected with 5 μg of peptide composition;

Group II: 3 subjects are injected with placebo and 6 subjects areinjected with 50 μg peptide composition;

Group III: 3 subjects are injected with placebo and 6 subjects areinjected with 500 μg of peptide composition.

After 4 weeks following the first injection, all subjects receive abooster inoculation at the same dosage.

The endpoints measured in this study relate to the safety andtolerability of the peptide composition as well as its immunogenicity.Cellular immune responses to the peptide composition are an index of theintrinsic activity of this the peptide composition, and can therefore beviewed as a measure of biological efficacy. The following summarize theclinical and laboratory data that relate to safety and efficacyendpoints.

Safety: The incidence of adverse events is monitored in the placebo anddrug treatment group and assessed in terms of degree and reversibility.

Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy,subjects are bled before and after injection. Peripheral bloodmononuclear cells are isolated from fresh heparinized blood byFicoll-Hypaque density gradient centrifugation, aliquoted in freezingmedia and stored frozen. Samples are assayed for CTL and HTL activity.

The vaccine is found to be both safe and efficacious.

Example 30 Phase II Trials in Patients Expressing 238P1B2

Phase II trials are performed to study the effect of administering theCTL-HTL peptide compositions to patients having cancer that expresses238P1B2. The main objectives of the trial are to determine an effectivedose and regimen for inducing CTLs in cancer patients that express238P1B2, to establish the safety of inducing a CTL and HTL response inthese patients, and to see to what extent activation of CTLs improvesthe clinical picture of these patients, as manifested, e.g., by thereduction and/or shrinking of lesions. Such a study is designed, forexample, as follows:

The studies are performed in multiple centers. The trial design is anopen-label, uncontrolled, dose escalation protocol wherein the peptidecomposition is administered as a single dose followed six weeks later bya single booster shot of the same dose. The dosages are 50, 500 and5,000 micrograms per injection. Drug-associated adverse effects(severity and reversibility) are recorded.

There are three patient groupings. The first group is injected with 50micrograms of the peptide composition and the second and third groupswith 500 and 5,000 micrograms of peptide composition, respectively. Thepatients within each group range in age from 21-65 and represent diverseethnic backgrounds. All of them have a tumor that expresses 238P1B2.

Clinical manifestations or antigen-specific T-cell responses aremonitored to assess the effects of administering the peptidecompositions. The vaccine composition is found to be both safe andefficacious in the treatment of 238P1B2-associated disease.

Example 31 Induction of CTL Responses Using a Prime Boost Protocol

A prime boost protocol similar in its underlying principle to that usedto confirm the efficacy of a DNA vaccine in transgenic mice, such asdescribed above in the Example entitled “The Plasmid Construct and theDegree to Which It Induces Immunogenicity,” can also be used for theadministration of the vaccine to humans. Such a vaccine regimen caninclude an initial administration of, for example, naked DNA followed bya boost using recombinant virus encoding the vaccine, or recombinantprotein/polypeptide or a peptide mixture administered in an adjuvant.

For example, the initial immunization may be performed using anexpression vector, such as that constructed in the Example entitled“Construction of ‘Minigene’ Multi-Epitope DNA Plasmids” in the form ofnaked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also beadministered using a gene gun. Following an incubation period of 3-4weeks, a booster dose is then administered. The booster can berecombinant fowlpox virus administered at a dose of 5-10⁷ to 5×10⁹ pfu.An alternative recombinant virus, such as an MVA, canarypox, adenovirus,or adeno-associated virus, can also be used for the booster, or thepolyepitopic protein or a mixture of the peptides can be administered.For evaluation of vaccine efficacy, patient blood samples are obtainedbefore immunization as well as at intervals following administration ofthe initial vaccine and booster doses of the vaccine. Peripheral bloodmononuclear cells are isolated from fresh heparinized blood byFicoll-Hypaque density gradient centrifugation, aliquoted in freezingmedia and stored frozen. Samples are assayed for CTL and HTL activity.

Analysis of the results indicates that a magnitude of responsesufficient to achieve a therapeutic or protective immunity against238P1B2 is generated.

Example 32 Administration of Vaccine Compositions Using Dendritic Cells(DC)

Vaccines comprising peptide epitopes of the invention can beadministered using APCs, or “professional” APCs such as DC. In thisexample, peptide-pulsed DC are administered to a patient to stimulate aCTL response in vivo. In this method, dendritic cells are isolated,expanded, and pulsed with a vaccine comprising peptide CTL and HTLepitopes of the invention. The dendritic cells are infused back into thepatient to elicit CTL and HTL responses in vivo. The induced CTL and HTLthen destroy or facilitate destruction, respectively, of the targetcells that bear the 238P1B2 protein from which the epitopes in thevaccine are derived.

For example, a cocktail of epitope-comprising peptides is administeredex vivo to PBMC, or isolated DC therefrom. A pharmaceutical tofacilitate harvesting of DC can be used, such as Progenipoietin™(Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC withpeptides, and prior to reinfusion into patients, the DC are washed toremove unbound peptides.

As appreciated clinically, and readily determined by one of skill basedon clinical outcomes, the number of DC reinfused into the patient canvary (see, e.g., Nature Med. 4:328, 1998; Nature Med. 2:52, 1996 andProstate 32:272, 1997). Although 2−50×10⁶ DC per patient are typicallyadministered, larger number of DC, such as 10⁷ or 10⁸ can also beprovided. Such cell populations typically contain between 50-90% DC.

In some embodiments, peptide-loaded PBMC are injected into patientswithout purification of the DC. For example, PBMC generated aftertreatment with an agent such as Progenipoietin™ are injected intopatients without purification of the DC. The total number of PBMC thatare administered often ranges from 10⁸ to 10¹⁰. Generally, the celldoses injected into patients is based on the percentage of DC in theblood of each patient, as determined, for example, by immunofluorescenceanalysis with specific anti-DC antibodies. Thus, for example, ifProgenipoietin™ mobilizes 2% DC in the peripheral blood of a givenpatient, and that patient is to receive 5×10⁶ DC, then the patient willbe injected with a total of 2.5×10⁸ peptide-loaded PBMC. The percent DCmobilized by an agent such as Progenipoietin™ is typically estimated tobe between 2-10%, but can vary as appreciated by one of skill in theart.

Ex Vivo Activation of CTL/HTL Responses

Alternatively, ex vivo CTL or HTL responses to 238P1B2 antigens can beinduced by incubating, in tissue culture, the patient's, or geneticallycompatible, CTL or HTL precursor cells together with a source of APC,such as DC, and immunogenic peptides. After an appropriate incubationtime (typically about 7-28 days), in which the precursor cells areactivated and expanded into effector cells, the cells are infused intothe patient, where they will destroy (CTL) or facilitate destruction(HTL) of their specific target cells, i.e., tumor cells.

Example 33 An Alternative Method of Identifying and ConfirmingMotif-Bearing Peptides

Another method of identifying and confirming motif-bearing peptides isto elute them from cells bearing defined MHC molecules. For example, EBVtransformed B cell lines used for tissue typing have been extensivelycharacterized to determine which HLA molecules they express. In certaincases these cells express only a single type of HLA molecule. Thesecells can be transfected with nucleic acids that express the antigen ofinterest, e.g. 238P1B2. Peptides produced by endogenous antigenprocessing of peptides produced as a result of transfection will thenbind to HLA molecules within the cell and be transported and displayedon the cell's surface. Peptides are then eluted from the HLA moleculesby exposure to mild acid conditions and their amino acid sequencedetermined, e.g., by mass spectral analysis (e.g., Kubo et al., J.Immunol. 152:3913, 1994). Because the majority of peptides that bind aparticular HLA molecule are motif-bearing, this is an alternativemodality for obtaining the motif-bearing peptides correlated with theparticular HLA molecule expressed on the cell.

Alternatively, cell lines that do not express endogenous HLA moleculescan be transfected with an expression construct encoding a single HLAallele. These cells can then be used as described, i.e., they can thenbe transfected with nucleic acids that encode 238P1B2 to isolatepeptides corresponding to 238P1B2 that have been presented on the cellsurface. Peptides obtained from such an analysis will bear motif(s) thatcorrespond to binding to the single HLA allele that is expressed in thecell.

As appreciated by one in the art, one can perform a similar analysis ona cell bearing more than one HLA allele and subsequently determinepeptides specific for each HLA allele expressed. Moreover, one of skillwould also recognize that means other than transfection, such as loadingwith a protein antigen, can be used to provide a source of antigen tothe cell.

Example 34 Complementary Polynucleotides

Sequences complementary to the 238P1B2-encoding sequences, or any partsthereof, are used to detect, decrease, or inhibit expression ofnaturally occurring 238P1B2. Although use of oligonucleotides comprisingfrom about 15 to 30 base pairs is described, essentially the sameprocedure is used with smaller or with larger sequence fragments.Appropriate oligonucleotides are designed using, e.g., OLIGO 4.06software (National Biosciences) and the coding sequence of 238P1B2. Toinhibit transcription, a complementary oligonucleotide is designed fromthe most unique 5′ sequence and used to prevent promoter binding to thecoding sequence. To inhibit translation, a complementary oligonucleotideis designed to prevent ribosomal binding to a 238P1B2-encodingtranscript.

Example 35 Purification of Naturally-Occurring or Recombinant 238P1B2Using 238P1B2 Specific Antibodies

Naturally occurring or recombinant 238P1B2 is substantially purified byimmunoaffinity chromatography using antibodies specific for 238P1B2. Animmunoaffinity column is constructed by covalently coupling anti-238P1B2antibody to an activated chromatographic resin, such as CNBr-activatedSEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin isblocked and washed according to the manufacturer's instructions.

Media containing 238P1B2 are passed over the immunoaffinity column, andthe column is washed under conditions that allow the preferentialabsorbance of 238P1B2 (e.g., high ionic strength buffers in the presenceof detergent). The column is eluted under conditions that disruptantibody/238P1B2 binding (e.g., a buffer of pH 2 to pH 3, or a highconcentration of a chaotrope, such as urea or thiocyanate ion), andGCR.P is collected.

Example 36 Identification of Molecules which Interact with 238P1B2

238P1B2, or biologically active fragments thereof, are labeled with 1211 Bolton-Hunter reagent. (See, e.g., Bolton et al. (1973) Biochem. J.133:529.) Candidate molecules previously arrayed in the wells of amulti-well plate are incubated with the labeled 238P1B2, washed, and anywells with labeled 238P1B2 complex are assayed. Data obtained usingdifferent concentrations of 238P1B2 are used to calculate values for thenumber, affinity, and association of 238P1B2 with the candidatemolecules.

Example 37 In Vivo Assay for 238P1B2 Tumor Growth Promotion

The effect of the 238P1B2 protein on tumor cell growth is evaluated invivo by gene overexpression in tumor-bearing mice. For example, SCIDmice are injected subcutaneously on each flank with 1×10⁶ of either PC3,DU145 or 3T3 cells containing tkNeo empty vector or 238P1B2. At leasttwo strategies can be used: (1) Constitutive 238P1B2 expression underregulation of a promoter such as a constitutive promoter obtained fromthe genomes of viruses such as polyoma virus, fowlpox virus (UK2,211,504 published 5 Jul. 1989), adenovirus (such as Adenovirus 2),bovine papilloma virus, avian sarcoma virus, cytomegalovirus, aretrovirus, hepatitis-B virus and Simian Virus 40 (SV40), or fromheterologous mammalian promoters, e.g., the actin promoter or animmunoglobulin promoter, provided such promoters are compatible with thehost cell systems, and (2) Regulated expression under control of aninducible vector system, such as ecdysone, tet, etc., provided suchpromoters are compatible with the host cell systems. Tumor volume isthen monitored at the appearance of palpable tumors and followed overtime to determine if 238P1B2-expressing cells grow at a faster rate andwhether tumors produced by 238P1B2-expressing cells demonstratecharacteristics of altered aggressiveness (e.g. enhanced metastasis,vascularization, reduced responsiveness to chemotherapeutic drugs).

Additionally, mice can be implanted with 1×10⁵ of the same cellsorthotopically to determine if 238P1B2 has an effect on local growth inthe prostate or on the ability of the cells to metastasize, specificallyto lungs, lymph nodes, and bone marrow.

The assay is also useful to determine the 238P1B2 inhibitory effect ofcandidate therapeutic compositions, such as for example, 238P1B2intrabodies, 238P1B2 antisense molecules and ribozymes.

Example 38 238P1B2 Monoclonal Antibody-Mediated Inhibition of ProstateTumors In Vivo

The significant expression of 238P1B2 in prostate cancer tissues and itsrestrictive expression in normal tissues, together with its expectedcell surface expression, makes 238P1B2 an excellent target for antibodytherapy. Similarly, 238P1B2 is a target for T cell-based immunotherapy.Thus, the therapeutic efficacy of anti-238P1B2 mAbs in human prostatecancer xenograft mouse models is evaluated by using human cancerxenografts (Craft, N., et al.,. Cancer Res, 1999. 59(19): p. 5030-6) andthe androgen independent recombinant cell line PC3-238P1B2 (see, e.g.,Kaighn, M. E., et al., Invest Urol, 1979. 17(1): p. 16-23).

Antibody efficacy on tumor growth and metastasis formation is studied,e.g., in a mouse orthotopic prostate cancer xenograft models and mousekidney xenograft models. The antibodies can be unconjugated, asdiscussed in this Example, or can be conjugated to a therapeuticmodality, as appreciated in the art. Anti-238P1B2 mAbs inhibit formationof androgen-independent PC3-238P1B2 tumor xenografts. Anti-238P1B2 mAbsalso retard the growth of established orthotopic tumors and prolongedsurvival of tumor-bearing mice. These results indicate the utility ofanti-238P1B2 mAbs in the treatment of local and advanced stages ofprostate cancer. (See, e.g., Saffran, D., et al., PNAS 10:1073-1078).

Administration of the anti-238P1B2 mAbs led to retardation ofestablished orthotopic tumor growth and inhibition of metastasis todistant sites, resulting in a significant prolongation in the survivalof tumor-bearing mice. These studies indicate that 238P1B2 as anattractive target for immunotherapy and demonstrate the therapeuticpotential of anti-238P1B2 mAbs for the treatment of local and metastaticprostate cancer. This example demonstrates that unconjugated 238P1B2monoclonal antibodies are effective to inhibit the growth of humanprostate tumor xenografts and human kidney xenografts grown in SCIDmice; accordingly a combination of such efficacious monoclonalantibodies is also effective.

Tumor Inhibition Using Multiple Unconjugated 238P1B2 mAbs

Materials and Methods

238P1B2 Monoclonal Antibodies:

Monoclonal antibodies are raised against 238P1B2 as described in theExample entitled “Generation of 238P1B2 Monoclonal Antibodies (mAbs).”The antibodies are characterized by ELISA, Western blot, FACS, andimmunoprecipitation for their capacity to bind 238P1B2. Epitope mappingdata for the anti-238P1B2 mAbs, as determined by ELISA and Westernanalysis, indicates that the antibodies recognize epitopes on the238P1B2 protein. Immunohistochemical analysis of prostate cancer tissuesand cells with these antibodies is performed.

The monoclonal antibodies are purified from ascites or hybridoma tissueculture supernatants by Protein-G Sepharose chromatography, dialyzedagainst PBS, filter sterilized, and stored at −20° C. Proteindeterminations are performed by a Bradford assay (Bio-Rad, Hercules,Calif.). A therapeutic monoclonal antibody or a cocktail comprising amixture of individual monoclonal antibodies is prepared and used for thetreatment of mice receiving subcutaneous or orthotopic injections ofLAPC-9 prostate tumor xenografts.

Cancer Xenografts and Cell Lines

Human cancer xenograft models as well as ICR-severe combinedimmunodeficient (SCID) mice injected with human cell lines expressing orlacking 238P1B2 are used to confirm the role of this gene in tumorgrowth and progression. Prostate xenograft tissue is passaged in 6- to8-week-old male SCID mice (Taconic Farms) by s.c. trocar implant (Craft,N., et al., supra). The prostate carcinoma cell line PC3 (American TypeCulture Collection) is maintained in RPMI supplemented with L-glutamineand 10% FBS.

PC3-238P1B2 and 3T3-238P1B2 cell populations are generated by retroviralgene transfer as described in Hubert, R. S., et al., STEAP: aprostate-specific cell-surface antigen highly expressed in humanprostate tumors. Proc Natl Acad Sci USA, 1999. 96(25): p. 14523-8.Anti-238P1B2 staining is detected by using an FITC-conjugated goatanti-mouse antibody (Southern Biotechnology Associates) followed byanalysis on a Coulter Epics-XL flow cytometer.

Xenograft Mouse Models.

Subcutaneous (s.c.) tumors are generated by injection of 1×10⁶ cells,such as PC3, PC3-238P1B2, 3T3 or 3T3-238P1B2 cells mixed at a 1:1dilution with Matrigel (Collaborative Research) in the right flank ofmale SCID mice. To test antibody efficacy on tumor formation, i.p.antibody injections are started on the same day as tumor-cellinjections. As a control, mice are injected with either purified mouseIgG (ICN) or PBS; or a purified monoclonal antibody that recognizes anirrelevant antigen not expressed in human cells. Tumor sizes aredetermined by vernier caliper measurements, and the tumor volume iscalculated as length×width×height. Mice with s.c. tumors greater than1.5 cm in diameter are sacrificed. PSA levels are determined by using aPSA ELISA kit (Anogen, Mississauga, Ontario). Circulating levels ofanti-238P1B2 mAbs are determined by a capture ELISA kit (BethylLaboratories, Montgomery, Tex.). (See, e.g., (Saffran, D., et al., PNAS10:1073-1078).

Orthotopic injections are performed under anesthesia by usingketamine/xylazine. For prostate orthotopic studies, an incision is madethrough the abdominal muscles to expose the bladder and seminalvesicles, which then are delivered through the incision to expose thedorsal prostate. PC3 cells (5×10⁵) mixed with Matrigel are injected intoeach dorsal lobe in a 10-μl volume. To monitor tumor growth, mice arebled on a weekly basis for determination of PSA levels. The mice aresegregated into groups for the appropriate treatments, with anti-238P1B2or control mAbs being injected i.p.

Anti-238P1B2 mAbs Inhibit Growth of 238P1B2-Expressing Xenograft-CancerTumors

The effect of anti-238P1B2 mAbs on tumor formation is tested by usingPC3-238P1B2 orthotopic models. As compared with the s.c. tumor model,the orthotopic model, which requires injection of tumor cells directlyin the mouse prostate or kidney, respectively, results in a local tumorgrowth, development of metastasis in distal sites, deterioration ofmouse health, and subsequent death (Saffran, D., et al., PNAS supra; Fu,X., et al., Int J Cancer, 1992. 52(6): p. 987-90; Kubota, T., J CellBiochem, 1994. 56(1): p. 4-8). The features make the orthotopic modelmore representative of human disease progression and allowed us tofollow the therapeutic effect of mAbs on clinically relevant end points.

Accordingly, tumor cells are injected into the mouse prostate or kidney,and 2 days later, the mice are segregated into two groups and treatedwith either: a) 200-500 μg, of anti-238P1B2 Ab, or b) PBS three timesper week for two to five weeks.

A major advantage of the orthotopic prostate-cancer model is the abilityto study the development of metastases. Formation of metastasis in micebearing established orthotopic tumors is studied by IHC analysis on lungsections using an antibody against a prostate-specific cell-surfaceprotein STEAP expressed at high levels in LAPC-9 xenografts (Hubert, R.S., et al., Proc Natl Acad Sci USA, 1999. 96(25): p. 14523-8).

Mice bearing established orthotopic 3T3-238P1B2 and PC3-238P1B2 tumorsare administered 1000 μg injections of either anti-238P1B2 mAb or PBSover a 4-week period. Mice in both groups are allowed to establish ahigh tumor burden, to ensure a high frequency of metastasis formation inmouse lungs. Mice then are killed and their prostate and lungs areanalyzed for the presence of tumor cells by IHC analysis.

These studies demonstrate a broad anti-tumor efficacy of anti-238P1B2antibodies on initiation and progression of prostate cancer in xenograftmouse models. Anti-238P1B2 antibodies inhibit tumor formation of bothandrogen-dependent and androgen-independent tumors, retard the growth ofalready established tumors, and prolong the survival of treated mice.Moreover, anti-238P1B2 mAbs demonstrate a dramatic inhibitory effect onthe spread of local prostate tumor to distal sites, even in the presenceof a large tumor burden. Thus, anti-238P1B2 mAbs are efficacious onmajor clinically relevant end points (tumor growth), prolongation ofsurvival, and health.

Example 39 Therapeutic and Diagnostic Use of Anti-238P1B2 Antibodies inHumans

Anti-238P1B2 monoclonal antibodies are safely and effectively used fordiagnostic, prophylactic, prognostic and/or therapeutic purposes inhumans. Western blot and immunohistochemical analysis of cancer tissuesand cancer xenografts with anti-238P1B2 mAb show strong extensivestaining in carcinoma but significantly lower or undetectable levels innormal tissues. Detection of 238P1B2 in carcinoma and in metastaticdisease demonstrates the usefulness of the mAb as a diagnostic and/orprognostic indicator. Anti-238P1B2 antibodies are therefore used indiagnostic applications such as immunohistochemistry of kidney biopsyspecimens to detect cancer from suspect patients.

As determined by flow cytometry, anti-238P1B2 mAb specifically binds tocarcinoma cells. Thus, anti-238P1B2 antibodies are used in diagnosticwhole body imaging applications, such as radioimmunoscintigraphy andradioimmunotherapy, (see, e.g., Potamianos S., et. al. Anticancer Res20(2A):925-948 (2000)) for the detection of localized and metastaticcancers that exhibit expression of 238P1B2. Shedding or release of anextracellular domain of 238P1B2 into the extracellular milieu, such asthat seen for alkaline phosphodiesterase B10 (Meerson, N. R., Hepatology27:563-568 (1998)), allows diagnostic detection of 238P1B2 byanti-238P1B2 antibodies in serum and/or urine samples from suspectpatients.

Anti-238P1B2 antibodies that specifically bind 238P1B2 are used intherapeutic applications for the treatment of cancers that express238P1B2. Anti-238P1B2 antibodies are used as an unconjugated modalityand as conjugated form in which the antibodies are attached to one ofvarious therapeutic or imaging modalities well known in the art, such asa prodrugs, enzymes or radioisotopes. In preclinical studies,unconjugated and conjugated anti-238P1B2 antibodies are tested forefficacy of tumor prevention and growth inhibition in the SCID mousecancer xenograft models, e.g., kidney cancer models AGS-K3 and AGS-K6,(see, e.g., the Example entitled “Monoclonal Antibody-mediatedInhibition of Prostate Tumors In vivo”). Conjugated and unconjugatedanti-238P1B2 antibodies are used as a therapeutic modality in humanclinical trials either alone or in combination with other treatments asdescribed in the following Examples.

Example 40 Human Clinical Trials for the Treatment and Diagnosis ofHuman Carcinomas Through Use of Human Anti-238P1B2 Antibodies In Vivo

Antibodies are used in accordance with the present invention whichrecognize an epitope on 238P1B2, and are used in the treatment ofcertain tumors such as those listed in Table I. Based upon a number offactors, including 238P1B2 expression levels, tumors such as thoselisted in Table I are presently preferred indications. In connectionwith each of these indications, three clinical approaches aresuccessfully pursued.

I.) Adjunctive therapy: In adjunctive therapy, patients are treated withanti-238P1B2 antibodies in combination with a chemotherapeutic orantineoplastic agent and/or radiation therapy. Primary cancer targets,such as those listed in Table I, are treated under standard protocols bythe addition anti-238P1B2 antibodies to standard first and second linetherapy. Protocol designs address effectiveness as assessed by reductionin tumor mass as well as the ability to reduce usual doses of standardchemotherapy. These dosage reductions allow additional and/or prolongedtherapy by reducing dose-related toxicity of the chemotherapeutic agent.Anti-238P1B2 antibodies are utilized in several adjunctive clinicaltrials in combination with the chemotherapeutic or antineoplastic agentsadriamycin (advanced prostrate carcinoma), cisplatin (advanced head andneck and lung carcinomas), taxol (breast cancer), and doxorubicin(preclinical).

II.) Monotherapy: In connection with the use of the anti-238P1B2antibodies in monotherapy of tumors, the antibodies are administered topatients without a chemotherapeutic or antineoplastic agent. In oneembodiment, monotherapy is conducted clinically in end stage cancerpatients with extensive metastatic disease. Patients show some diseasestabilization. Trials demonstrate an effect in refractory patients withcancerous tumors.

III.) Imaging Agent: Through binding a radionuclide (e.g., iodine oryttrium (I¹³¹, Y⁹⁰) to anti-238P1B2 antibodies, the radiolabeledantibodies are utilized as a diagnostic and/or imaging agent. In such arole, the labeled antibodies localize to both solid tumors, as well as,metastatic lesions of cells expressing 238P1B2. In connection with theuse of the anti-238P1B2 antibodies as imaging agents, the antibodies areused as an adjunct to surgical treatment of solid tumors, as both apre-surgical screen as well as a post-operative follow-up to determinewhat tumor remains and/or returns. In one embodiment, a (111 In)-238P1B2antibody is used as an imaging agent in a Phase I human clinical trialin patients having a carcinoma that expresses 238P1B2 (by analogy see,e.g., Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991)). Patients arefollowed with standard anterior and posterior gamma camera. The resultsindicate that primary lesions and metastatic lesions are identified

Dose and Route of Administration

As appreciated by those of ordinary skill in the art, dosingconsiderations can be determined through comparison with the analogousproducts that are in the clinic. Thus, anti-238P1B2 antibodies can beadministered with doses in the range of 5 to 400 mg/m², with the lowerdoses used, e.g., in connection with safety studies. The affinity ofanti-238P1B2 antibodies relative to the affinity of a known antibody forits target is one parameter used by those of skill in the art fordetermining analogous dose regimens. Further, anti-238P1B2 antibodiesthat are fully human antibodies, as compared to the chimeric antibody,have slower clearance; accordingly, dosing in patients with such fullyhuman anti-238P1B2 antibodies can be lower, perhaps in the range of 50to 300 mg/m², and still remain efficacious. Dosing in mg/m², as opposedto the conventional measurement of dose in mg/kg, is a measurement basedon surface area and is a convenient dosing measurement that is designedto include patients of all sizes from infants to adults.

Three distinct delivery approaches are useful for delivery ofanti-238P1B2 antibodies. Conventional intravenous delivery is onestandard delivery technique for many tumors. However, in connection withtumors in the peritoneal cavity, such as tumors of the ovaries, biliaryduct, other ducts, and the like, intraperitoneal administration mayprove favorable for obtaining high dose of antibody at the tumor and toalso minimize antibody clearance. In a similar manner, certain solidtumors possess vasculature that is appropriate for regional perfusion.Regional perfusion allows for a high dose of antibody at the site of atumor and minimizes short term clearance of the antibody.

Clinical Development Plan (CDP)

Overview: The CDP follows and develops treatments of anti-238P1B2antibodies in connection with adjunctive therapy, monotherapy, and as animaging agent. Trials initially demonstrate safety and thereafterconfirm efficacy in repeat doses. Trails are open label comparingstandard chemotherapy with standard therapy plus anti-238P1B2antibodies. As will be appreciated, one criteria that can be utilized inconnection with enrollment of patients is 238P1B2 expression levels intheir tumors as determined by biopsy.

As with any protein or antibody infusion-based therapeutic, safetyconcerns are related primarily to (i) cytokine release syndrome, i.e.,hypotension, fever, shaking, chills; (ii) the development of animmunogenic response to the material (i.e., development of humanantibodies by the patient to the antibody therapeutic, or HAHAresponse); and, (iii) toxicity to normal cells that express 238P1B2.Standard tests and follow-up are utilized to monitor each of thesesafety concerns. Anti-238P1B2 antibodies are found to be safe upon humanadministration.

Example 41 Human Clinical Trial Adjunctive Therapy with HumanAnti-238P1B2 Antibody and Chemotherapeutic Agent

A phase I human clinical trial is initiated to assess the safety of sixintravenous doses of a human anti-238P1B2 antibody in connection withthe treatment of a solid tumor, e.g., a cancer of a tissue listed inTable I. In the study, the safety of single doses of anti-238P1B2antibodies when utilized as an adjunctive therapy to an antineoplasticor chemotherapeutic agent, such as cisplatin, topotecan, doxorubicin,adriamycin, taxol, or the like, is assessed. The trial design includesdelivery of six single doses of an anti-238P1B2 antibody with dosage ofantibody escalating from approximately about 25 mg/m² to about 275 mg/m²over the course of the treatment in accordance with the followingschedule:

Day 0 Day 7 Day 14 Day 21 Day 28 Day 35 mAb Dose 25 75 125 175 225 275mg/m² mg/m² mg/m² mg/m² mg/m² mg/m² Chemotherapy + + + + + + (standarddose)

Patients are closely followed for one-week following each administrationof antibody and chemotherapy. In particular, patients are assessed forthe safety concerns mentioned above: (i) cytokine release syndrome,i.e., hypotension, fever, shaking, chills; (ii) the development of animmunogenic response to the material (i.e., development of humanantibodies by the patient to the human antibody therapeutic, or HAHAresponse); and, (iii) toxicity to normal cells that express 238P1B2.Standard tests and follow-up are utilized to monitor each of thesesafety concerns. Patients are also assessed for clinical outcome, andparticularly reduction in tumor mass as evidenced by MRI or otherimaging.

The anti-238P1B2 antibodies are demonstrated to be safe and efficacious,Phase II trials confirm the efficacy and refine optimum dosing.

Example 42 Human Clinical Trial: Monotherapy with Human Anti-238P1B2Antibody

Anti-238P1B2 antibodies are safe in connection with the above-discussedadjunctive trial, a Phase II human clinical trial confirms the efficacyand optimum dosing for monotherapy. Such trial is accomplished, andentails the same safety and outcome analyses, to the above-describedadjunctive trial with the exception being that patients do not receivechemotherapy concurrently with the receipt of doses of anti-238P1B2antibodies.

Example 43 Human Clinical Trial: Diagnostic Imaging with Anti-238P1B2Antibody

Once again, as the adjunctive therapy discussed above is safe within thesafety criteria discussed above, a human clinical trial is conductedconcerning the use of anti-238P1B2 antibodies as a diagnostic imagingagent. The protocol is designed in a substantially similar manner tothose described in the art, such as in Divgi et al. J. Natl. CancerInst. 83:97-104 (1991). The antibodies are found to be both safe andefficacious when used as a diagnostic modality.

Example 44 Homology Comparison of 238P1B2 to Known Sequences

The 238P1B2 gene is homologous to a cloned and sequenced gene, namelythe mouse olfactory receptor MOR14-1 (gi 18479244) (Zhang X, FiresteinS. Nat. Neurosci. 2002, 5:124), showing 83% identity and 90% homology tothat gene product (FIG. 4A; FIG. 4C). The 238P1B2 protein shows 78%identity and 87% homology to another mouse olfactory receptor, namelyMOR14-10 (gi 18480766). The closest human homolog to 238P1B2 is thehuman olfactory receptor 5BETA12 (51I2, gi 17456801), with 61% identityand 79% homology (FIG. 4E). Comparison of 238P1B2 to another member ofthe human olfactory receptor family, namely 101P3A11 (reference AGSpatent), the 238P1B2 protein shows 48% identity and 70% homology to101P3A11, with the first amino acid of 238P1B2 aligning with aa 62 of101P3A11. The 238P1B2 variant 1A protein consists of 254 amino acids,with calculated molecular weight of 28.5 kDa, and pI of 9.2. 238P1B2 isa cell surface protein with some localization to the mitochondria andendoplasmic reticulum. Three forms of the 238P1B2 protein have beenidentified, with variant 238P1B2 V2 containing a isoleucine to threoninepoint mutation at amino acid 225, and variant 238P1B2 V1B containing anadditional 62 aa at its amino-terminus (FIG. 4F). While 238P1B2 V1A isprojected to have 6 transmembrane domains, 238P1B2 V1B contains 7transmembrane domains, with the N-terminus oriented extracellularly andthe C-terminus being intracellular (Table XXII, FIG. 13).

Motif analysis revealed the presence of several known motifs, includinga 7 transmembrane olfactory receptor GPCR motif and a fibronectin TypeIII repeat. Proteins that are members of the G-protein coupled receptorfamily exhibit an extracellular amino-terminus, three extracellularloops, three intracellular loops and an intracellular carboxyl terminus.G-protein coupled receptors are seven-transmembrane receptors that arestimulated by polypeptide hormones, neurotransmitters, chemokines andphospholipids (Civelli O et al, Trends Neurosci. 2001, 24:230; Vrecl Met al., Mol. Endocrinol. 1998, 12:1818). Ligand binding traditionallyoccurs between the first and second extracellular loops of the GPCR.Upon ligand binding GPCRs transduce signals across the cell surfacemembrane by associating with trimeric G proteins. Their signals aretransmitted via trimeric guanine-nucleotide binding proteins (Gproteins) to cell surface receptor, effector enzymes or ion channels(Simon et al., 1991, Science 252: 802). Signal transduction andbiological output mediated by GPCR can be modulated through variousmechanisms including peptide mimics, small molecule inhibitors and GPCRkinases or GRK (Pitcher J A et al, J Biol. Chem. 1999, 3; 274:34531;Fawzi A B, et al. 2001, Mol. Pharmacol., 59:30).

Recently, GPCRs have also been shown to link to mitogenic signalingpathways of tyrosine kinases (Luttrell et al., 1999, Science 283: 655;Luttrell et al., 1999 Curr Opin Cell Biol 11: 177). GPCRs are regulatedby phosphorylation mediated by GPCR kinases (GRKs), which themselves areindirectly activated by the GPCRs (Pitcher et al., 1998, Ann. Rev.Biochem. 67: 653). Olfactory GPCRs transmit their signals by activatingthe cAMP pathway via adenylate cyclase resulting in downstream signalingto protein kinase A, and by activating the phospholipase C pathway bygenerating inositol 1,4,5-trisphosphate (IP3) and diacyl-glycerol (DAG)(Breer, 1993, Ciba Found Symp 179: 97; Bruch, 1996, Comp Biochem PhysiolB Biochem Mol Biol 113:451). IP3 results in an increase in intracellularcalcium, while DAG activates protein kinase C.

Recent studies have associated GPCRs with cellular transformation. Inparticular, KSHV G protein-coupled receptor was found to transform NIH3T3 cells in vitro and induces multifocal KS-like lesions inKSHV-GPCR-transgenic mice (Schwarz M, Murphy P M. J Immunol 2001,167:505). KSHV-GPCR was capable of producing its effect on endothelialcells and fibroblasts by activating defined signaling pathways,including the AKT survival pathway (Montaner S et al, Cancer Res 2001,61:2641). In addition, KSHV-GPCR induced the activation of mitogenicpathways such as AP-1 and NFkB, resulting in the expression ofpro-inflammatory genes (Schwarz M, Murphy P M. J Immunol 2001, 167:505).Other GPCRs associated with tumor formation include G2A, and PAR-1,which has been found to induce transformation of NIH 3T3 cells(Whitehead I P et al, Oncogene 2001, 20:1547).

Fibronectin repeat regions are motifs that mediate binding to a varietyof substances such as heparin, collagen, fibrin and fibronectinreceptors on cell surfaces. Due to their binding capacity fibronectinsare involved in cell adhesion, cell differentiation, spreading,migration, and tumor metastasis (Nykvist P et al, J Biol Chem 2001,276:38673; Danen E H, Yamada K M. J Cell Physiol 2001, 189:1; NabeshimaK et al, Histol Histopathol 1999, 14:1183). In addition, fibronectinenhances angiogenesis and de novo blood vessel formation by regulatingthe migration of endothelial cells, which constitute essentialcomponents of blood vessels (Urbich C et al, Arterioscler Thromb VascBiol 2002, 22:69), thereby enhancing tumor growth and survival.

This information indicates that 238P1B2 plays a role in thetransformation of mammalian cells, induces mitogenic responses includingactivation of various signaling pathways, and regulates genetranscription by transmitting cell surface signals to the nucleus.Accordingly, when 238P1B2 functions as a regulator of celltransformation, tumor formation, or as a modulator of transcriptioninvolved in activating genes associated with inflammation, tumorigenesisor proliferation, 238P1B2 is used for therapeutic, diagnostic,prognostic and/or preventative purposes. In addition, when a molecule,such as a variant or polymorphism of 238P1B2 is expressed in canceroustissues, it is used for therapeutic, diagnostic, prognostic and/orpreventative purposes.

Example 45 Identification and Confirmation of Potential SignalTransduction Pathways

Many mammalian proteins have been reported to interact with signalingmolecules and to participate in regulating signaling pathways. (J.Neurochem. 2001; 76:217-223). In particular, GPCRs have been reported toactivate MAK cascades as well as G proteins, and have been associatedwith the EGFR pathway in epithelial cells (Naor, Z., et al, TrendsEndocrinol Metab. 2000, 11:91; Vacca F et al, Cancer Res. 2000, 60:5310;Della Rocca G J et al, J Biol. Chem. 1999, 274:13978). Usingimmunoprecipitation and Western blotting techniques, proteins areidentified that associate with 238P1B2 and mediate signaling events.Several pathways known to play a role in cancer biology can be regulatedby 238P1B2, including phospholipid pathways such as PI3K, AKT, etc.;adhesion and migration pathways, including FAK, Rho, Rac-1, etc.; andmitogenic/survival cascades such as ERK, p38, etc. (Cell Growth Differ.2000, 11:279; J Biol. Chem. 1999, 274:801; Oncogene. 2000, 19:3003, J.Cell Biol. 1997, 138:913).

Several GPCRs have been shown to transactivate receptor tyrosine kinasesassociated with the cell membrane, such as the EGF receptor (EGFR)(Pierce K L et al, J Biol. Chem. 2001, 276:23155; Nath D et al, J CellSci. 2001, 114:1213). In order to determine whether 238P1B2 signalingresults in the activation of EGFR, cells are grown in media alone or inthe presence of the EGFR inhibitor AG1517. EGFR phosphorylation iscompared in control and treated cells. Similarly, cross talk between238P1B2 and EGFR pathways is investigated.

To confirm that 238P1B2 directly or indirectly activates known signaltransduction pathways in cells, luciferase (luc) based transcriptionalreporter assays are carried out in cells expressing individual genes.These transcriptional reporters contain consensus-binding sites forknown transcription factors that lie downstream of well-characterizedsignal transduction pathways. The reporters and examples of theseassociated transcription factors, signal transduction pathways, andactivation stimuli are listed below.

1. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK; growth/apoptosis/stress

2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation

3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress

4. ARE-luc, androgen receptor; steroids/MAPK;growth/differentiation/apoptosis

5. p53-luc, p53; SAPK; growth/differentiation/apoptosis

6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress

Gene-mediated effects can be assayed in cells showing mRNA expression.Luciferase reporter plasmids can be introduced by lipid-mediatedtransfection (TFX-50, Promega). Luciferase activity, an indicator ofrelative transcriptional activity, is measured by incubation of cellextracts with luciferin substrate and luminescence of the reaction ismonitored in a luminometer.

Signaling pathways activated by 238P1B2 are mapped and used for theidentification and validation of therapeutic targets. When 238P1B2 isinvolved in cell signaling, it is used as target for diagnostic,prognostic, preventative and/or therapeutic purposes.

Example 46 238P1B2 Functions as a GPCR

Sequence and homology analysis of 238P1B2 indicate that the 238P1B2protein is a member of the olfactory receptor family of GPCR. Olfactoryreceptors are known to regulate biological responses by activatingadenylate cyclase. In order to confirm that 238P1B2 functions as a GPCRand mediates the activation of adenylate cyclase, cAMP accumulation inPC3 and PC3-238P1B2 cells are compared in cells grown in the presence orabsence of fetal bovine serum (FBS). The cells are lysed andintracellular concentration of cAMP are measured using a commerciallyavailable enzyme immunoassay (EIA). Calculations of cAMP concentrationswere based on OD450 of the standard curve. Similarly, the same assay canbe used to determine whether the induction of cAMP accumulation by238P1B2 is inhibited by GPCR inhibitors such as pertussis toxin.

GPCR transmit their signal by activating trimeric G proteins. Once GPCRsare activated, the associated Ga subunit binds GTP, dissociates from thereceptor and participates in downstream signaling events (Schild D andRestrepo D. Physiol Rev. 1998, 78:429-66). In order to determine thatinhibition of Ga subunits has an effect on 238P1B2 mediated cell growth,the effect of Ga inhibitors on the proliferation of 3T3-238P1B2 andPC3-238P1B2 cells is investigated. Control and 238P1B2-expressing cellsare grown in the presence or absence of suramin or its derivative NF 449(Sigma). Cells are analyzed for proliferation using an MTT-like assay.

When 238P1B2 functions as a GPCR, it is used as target for diagnostic,prognostic, preventative and/or therapeutic purposes.

Example 47 Involvement in Tumor Progression

The 238P1B2 gene can contribute to the growth of cancer cells. The roleof 238P1B2 in tumor growth is confirmed in a variety of primary andtransfected cell lines including prostate as well as NIH 3T3 cellsengineered to stably express 238P1B2. Parental cells lacking 238P1B2 andcells expressing 238P1B2 are evaluated for cell growth using awell-documented proliferation assay (Fraser S P, Grimes J A, Djamgoz MB. Prostate. 2000; 44:61, Johnson D E, Ochieng J, Evans S L. AnticancerDrugs. 1996, 7:288). To confirm that 238P1B2 mediates enhancedproliferation by way of its GPCR activity, control cells and cellsexpressing 238P1B2 are grown in the presence or absence of pertussistoxin, and evaluated for their proliferative capability using the sameassay described above.

To confirm the role of 238P1B2 in the transformation process, its effectin colony forming assays is investigated. Parental NIH-3T3 cells lacking238P1B2 are compared to NIH-3T3 cells expressing 238P1B2, using a softagar assay under stringent and more permissive conditions (Song Z. etal., Cancer Res. (2000) 60:6730).

To confirm the role of 238P1B2 in invasion and metastasis of cancercells, a well-established assay is used, e.g., a Transwell Insert Systemassay (Becton Dickinson) (Cancer Res. 1999; 59:6010). Control cells,including prostate and fibroblast cell lines lacking 238P1B2 arecompared to cells expressing 238P1B2. Cells are loaded with thefluorescent dye, calcein, and plated in the top well of the Transwellinsert coated with a basement membrane analog. Invasion is determined byfluorescence of cells in the lower chamber relative to the fluorescenceof the entire cell population.

238P1B2 can also play a role in cell cycle and apoptosis. Parental cellsand cells expressing 238P1B2 are compared for differences in cell cycleregulation using a well-established BrdU assay (Abdel-Malek Z A. J CellPhysiol. 1988, 136:247). In short, cells grown under both optimal (fullserum) and limiting (low serum) conditions are labeled with BrdU andstained with anti-BrdU Ab and propidium iodide. Cells are analyzed forentry into the G1, S, and G2M phases of the cell cycle. Alternatively,the effect of stress on apoptosis is evaluated in control parental cellsand cells expressing 238P1B2, including normal and tumor prostate cells.Engineered and parental cells are treated with various chemotherapeuticagents, such as etoposide, flutamide, etc, and protein synthesisinhibitors, such as cycloheximide. Cells are stained with annexin V-FITCand cell death is measured by FACS analysis. The modulation of celldeath by 238P1B2 can play a critical role in regulating tumorprogression and tumor load.

When 238P1B2 plays a role in cell growth, transformation, invasion orapoptosis, it is used as a target for diagnostic, prognostic,preventative and/or therapeutic purposes.

Example 48 Involvement in Angiogenesis

Angiogenesis or new capillary blood vessel formation is necessary fortumor growth (Hanahan D, Folkman J. Cell. 1996, 86:353; Folkman J.Endocrinology. 1998 139:441). Based on the effect of phosphodiesteraseinhibitors on endothelial cells, 238P1B2 plays a role in angiogenesis(DeFouw L et al, Microvasc Res 2001, 62:263). Several assays have beendeveloped to measure angiogenesis in vitro and in vivo, such as thetissue culture assays of endothelial cell tube formation and endothelialcell proliferation. Using these assays as well as in vitroneo-vascularization, the role of 238P1B2 in angiogenesis, enhancement orinhibition, is confirmed.

For example, endothelial cells engineered to express 238P1B2 areevaluated using tube formation and proliferation assays. The effect of238P1B2 is also confirmed in animal models in vivo. For example, cellseither expressing or lacking 238P1B2 are implanted subcutaneously inimmunocompromised mice. Endothelial cell migration and angiogenesis areevaluated 5-15 days later using immunohistochemistry techniques. 238P1B2affects angiogenesis, and it is used as a target for diagnostic,prognostic, preventative and/or therapeutic purposes

Example 49 Regulation of Transcription

The cell surface localization of 238P1B2 and its similarity to GPCRsindicate that 238P1B2 is effectively used as a modulator of thetranscriptional regulation of eukaryotic genes. Regulation of geneexpression is confirmed, e.g., by studying gene expression in cellsexpressing or lacking 238P1B2. For this purpose, two types ofexperiments are performed.

In the first set of experiments, RNA from parental and238P1B2-expressing cells are extracted and hybridized to commerciallyavailable gene arrays (Clontech) (Smid-Koopman E et al. Br J Cancer.2000. 83:246). Resting cells as well as cells treated with FBS orandrogen are compared. Differentially expressed genes are identified inaccordance with procedures known in the art. The differentiallyexpressed genes are then mapped to biological pathways (Chen K et al.Thyroid. 2001. 11:41.).

In the second set of experiments, specific transcriptional pathwayactivation is evaluated using commercially available (Stratagene)luciferase reporter constructs including: NFkB-luc, SRE-luc, ELK1-luc,ARE-luc, p53-luc, and CRE-luc. These transcriptional reporters containconsensus binding sites for known transcription factors that liedownstream of well-characterized signal transduction pathways, andrepresent a good tool to ascertain pathway activation and screen forpositive and negative modulators of pathway activation.

Thus, 238P1B2 plays a role in gene regulation, and it is used as atarget for diagnostic, prognostic, preventative and/or therapeuticpurposes.

Example 50 Involvement in Cell Adhesion

Cell adhesion plays a critical role in tissue colonization andmetastasis. Based on the presence of a fibronectin repeat in itsC-terminus, 238P1B2 can participate in cellular organization, and as aconsequence affects cell adhesion and motility. To confirm that 238P1B2regulates cell adhesion, control cells lacking 238P1B2 are compared tocells expressing 238P1B2, using techniques previously described (see,e.g., Haier et al, Br. J. Cancer. 1999, 80:1867; Lehr and Pienta, J.Natl. Cancer Inst. 1998, 90:118). Briefly, in one embodiment, cellslabeled with a fluorescent indicator, such as calcein, are incubated ontissue culture wells coated with media alone or with matrix proteins.Adherent cells are detected by fluorimetric analysis and percentadhesion is calculated. In another embodiment, cells lacking orexpressing 238P1B2 are analyzed for their ability to mediate cell-celladhesion using similar experimental techniques as described above. Bothof these experimental systems are used to identify proteins, antibodiesand/or small molecules that modulate cell adhesion to extracellularmatrix and cell-cell interaction. Cell adhesion plays a critical role intumor growth, progression, and colonization, and 238P1B2 is involved inthese processes. Thus, it serves as a diagnostic, prognostic,preventative and/or therapeutic modality.

Example 51 Protein-Protein Association

Several GPCRs have been shown to interact with other proteins, therebyregulating signal transduction, gene transcription, transformation andcell adhesion (Sexton P M et al, Cell Signal. 2001, 13:73; Turner C E, JCell Sci. 2000, 23:4139). Using immunoprecipitation techniques as wellas two yeast hybrid systems, proteins are identified that associate with238P1B2. Immunoprecipitates from cells expressing 238P1B2 and cellslacking 238P1B2 are compared for specific protein-protein associations.

Studies are performed to confirm the extent of association of 238P1B2with effector molecules, such as nuclear proteins, transcriptionfactors, kinases, phosphates etc. Studies comparing 238P1B2 positive and238P1B2 negative cells as well as studies comparing unstimulated/restingcells and cells treated with epithelial cell activators, such ascytokines, growth factors, androgen and anti-integrin Ab reveal uniqueinteractions.

In addition, protein-protein interactions are confirmed using two yeasthybrid methodology (Curr Opin Chem. Biol. 1999, 3:64). A vector carryinga library of proteins fused to the activation domain of a transcriptionfactor is introduced into yeast expressing a 238P1B2-DNA-binding domainfusion protein and a reporter construct. Protein-protein interaction isdetected by calorimetric reporter activity. Specific association witheffector molecules and transcription factors directs one of skill to themode of action of 238P1B2, and thus identifies therapeutic, prognostic,preventative and/or diagnostic targets for cancer. This and similarassays are also used to identify and screen for small molecules thatinteract with 238P1B2.

Thus it is found that 238P1B2 associates with proteins and smallmolecules. Accordingly, 238P1B2 and these proteins and small moleculesare used for diagnostic, prognostic, preventative and/or therapeuticpurposes.

Throughout this application, various website data content, publications,patent applications and patents are referenced. (Websites are referencedby their Uniform Resource Locator, or URL, addresses on the World WideWeb.) The disclosures of each of these references are herebyincorporated by reference herein in their entireties.

The present invention is not to be limited in scope by the embodimentsdisclosed herein, which are intended as single illustrations ofindividual aspects of the invention, and any that are functionallyequivalent are within the scope of the invention. Various modificationsto the models and methods of the invention, in addition to thosedescribed herein, will become apparent to those skilled in the art fromthe foregoing description and teachings, and are similarly intended tofall within the scope of the invention. Such modifications or otherembodiments can be practiced without departing from the true scope andspirit of the invention.

TABLES:

TABLE I: Tissues that Express 238P1B2 When Malignant

Prostate

TABLE II AMINO ACID ABBREVIATIONS SINGLE LETTER THREE LETTER FULL NAME FPhe phenylalanine L Leu leucine S Ser serine Y Tyr tyrosine C Cyscysteine W Trp tryptophan P Pro proline H His histidine Q Gln glutamineR Arg arginine I Ile isoleucine M Met methionine T Thr threonine N Asnasparagine K Lys lysine V Val valine A Ala alanine D Asp aspartic acid EGlu glutamic acid G Gly glycine

TABLE III Amino Acid Substitution Matrix A C D E F G H I K L M N P Q R ST V W Y . 4 0 −2 −1 −2 0 −2 −1 −1 −1 −1 −2 −1 −1 −1 1 0 0 −3 −2 A 9 −3−4 −2 −3 −3 −1 −3 −1 −1 −3 −3 −3 −3 −1 −1 −1 −2 −2 C 6 2 −3 −1 −1 −3 −1−4 −3 1 −1 0 −2 0 −1 −3 −4 −3 D 5 −3 −2 0 −3 1 −3 −2 0 −1 2 0 0 −1 −2 −3−2 E 6 −3 −1 0 −3 0 0 −3 −4 −3 −3 −2 −2 −1 1 3 F 6 −2 −4 −2 −4 −3 0 −2−2 −2 0 −2 −3 −2 −3 G 8 −3 −1 −3 −2 1 −2 0 0 −1 −2 −3 −2 2 H 4 −3 2 1 −3−3 −3 −3 −2 −1 3 −3 −1 I 5 −2 −1 0 −1 1 2 0 −1 −2 −3 −2 K 4 2 −3 −3 −2−2 −2 −1 1 −2 −1 L 5 −2 −2 0 −1 −1 −1 1 −1 −1 M 6 −2 0 0 1 0 −3 −4 −2 N7 −1 −2 −1 −1 −2 −4 −3 P 5 1 0 −1 −2 −2 −1 Q 5 −1 −1 −3 −3 −2 R 4 1 −2−3 −2 S 5 0 −2 −2 T 4 −3 −1 V 11 2 W 7 Y Adapted from the GCG Software9.0 BLOSUM62 amino acid substitution matrix (block substitution matrix).The higher the value, the more likely a substitution is found inrelated, natural proteins.

TABLE IV (A) POSITION POSITION C Terminus POSITION 3 (Primary (Primary 2(Primary Anchor) Anchor) Anchor) SUPERMOTIFS A1 TI LVMS FWY A2 LIVM ATQIV MATL A3 VSMA TLI RK A24 YF WIVLMT FI YWLM B7 P VILF MWYA B27 RHK FYLWMIVA B44 E D FWYLIMVA B58 ATS FWY LIVMA B62 QL IVMP FWYMIVLA MOTIFS A1TSM Y A1 DE AS Y A2.1 LM VQIAT V LIMAT A3 LMVISATF CGD KYR HFA A11VTMLISAGN CDF K RYH A24 YFWM FLIW A*3101 MVT ALIS R K A*3301 MVALF ISTRK A*6801 AVT MSLI RK B*0702 P LMF WYAIV B*3501 P LMFWY IVA B51 P LIVFWYAM B*5301 P IMFWY ALV B*5401 P ATIV LMFWY Bolded residues arepreferred, italicized residues are less preferred: A peptide isconsidered motif-bearing if it has primary anchors at each primaryanchor position for a motif or supermotif as specified in the abovetable.

TABLE IV (B) HLA CLASS II SUPERMOTIF 1 6 9 W, F, Y, V, .I, L A, V, I, L,P, C, S, T A, V, I, L, C, S, T, M, Y

TABLE IV (C) HLA Class II Motifs MOTIFS 1° anchor 1 2 3 4 5 1° anchor 67 8 9 DR4 preferred FMYLIVW M T I VSTCPALIM MH MH deleterious W R WDEDR1 preferred MFLIVWY PAMQ VMATSPLIC M AVM deleterious C CH FD CWD GDE DDR7 preferred MFLIVWY M W A IVMSACTPL M IV deleterious C G GRD N G DR3MOTIFS 1° anchor 1 2 3 1° anchor 4 5 1° anchor 6 motif a preferredLIVMFY D motif b preferred LIVMFAY DNQEST KRH DR Supermotif MFLIVWYVMSTACPLI Italicized residues indicate less preferred or “tolerated”residues

TABLE IV (D) HLA Class I Supermotifs SUPER- MOTIFS POSITION: 1 2 3 4 5 67 8 C-terminus A1 1° Anchor 1° Anchor TILVMS FWY A2 1° Anchor 1° AnchorLIVMATQ LIVMAT A3 preferred 1° Anchor YFW YFW YFW P 1° Anchor VSMATLI(4/5) (3/5) (4/5) (4/5) RK deleterious DE (3/5); DE P (5/5) (4/5) A24 1°Anchor 1° Anchor YFWIVLMT FIYWLM B7 preferred FWY (5/5) 1° Anchor FWYFWY 1° Anchor LIVM (3/5) P (4/5) (3/5) VILFMWYA deleterious DE (3/5); DEG QN DE P(5/5); (3/5) (4/5) (4/5) (4/5) G(4/5); A(3/5); QN(3/5) B27 1°Anchor 1° Anchor RHK FYLWMIVA B44 1° Anchor 1° Anchor ED FWYLIMVA B58 1°Anchor 1° Anchor ATS FWYLIVMA B62 1° Anchor 1° Anchor QLIVMP FWYMIVLA

TABLE IV (E) HLA Class I Motifs POSITION 1 2 3 4 5 6 A1 preferred GFYW1° Anchor DEA YFW P 9-mer STM deleterious DE RHKLIVMP A G A A1 preferredGRHK ASTCLIVM 1° Anchor GSTC ASTC 9-mer DEAS deleterious A RHKDEPYFW DEPQN RHK A1 preferred YFW 1° Anchor DEAQN A YFWQN 10-mer STM deleteriousGP RHKGLIVM DE RHK QNA A1 preferred YFW STCLIVM 1° Anchor A YFW 10-merDEAS deleterious RHK RHKDEPYFW P G A2.1 preferred YFW 1° Anchor YFW STCYFW 9-mer LMIVQAT deleterious DEP DERKH RKH A2.1 preferred AYFW 1°Anchor LVIM G G 10-mer LMIVQAT deleterious DEP DE RKHA P A3 preferredRHK 1° Anchor YFW PRHKYFW A YFW LMVISATFCGD deleterious DEP DE A11preferred A 1° Anchor YFW YFW A YFW VTLMISAGNCDF deleterious DEP A24preferred YFWRHK 1° Anchor STC 9-mer YFWM deleterious DEG DE G QNP DERHKA24 preferred 1° Anchor P YFWP 10-mer YFWM deleterious GDE QN RHK DEA3101 preferred RHK 1° Anchor YFW P YFW MVTALIS deleterious DEP DE ADEDE A3301 preferred 1° Anchor YFW MVALFIST deleterious GP DE A6801preferred YFWSTC 1° Anchor YFWLIVM AVTMSLI deleterious GP DEG RHK B0702preferred RHKFWY 1° Anchor RHK RHK RHK P deleterious DEQNP DEP DE DE GDEB3501 preferred FWYLIVM 1° Anchor FWY P deleterious AGP G G B51preferred LIVMFWY 1° Anchor FWY STC FWY P deleterious AGPDERHKSTC DE GB5301 preferred LIVMFWY 1° Anchor FWY STC FWY P deleterious AGPQN GB5401 preferred FWY 1° Anchor FWYLIVM LIVM P deleterious GPQNDE GDESTCRHKDE DE 9 or C- POSITION 7 8 C-terminus terminus A1 preferred DEQN YFW1° Anchor 9-mer Y deleterious A1 preferred LIVM DE 1° Anchor 9-mer Ydeleterious PG GP A1 preferred PASTC GDE P 1° Anchor 10-mer Ydeleterious RHKYFW RHK A A1 preferred PG G YFW 1° Anchor 10-mer Ydeleterious PRHK QN A2.1 preferred A P 1° Anchor 9-mer VLIMATdeleterious DERKH A2.1 preferred FYWLVIM 1° Anchor 10-mer VLIMATdeleterious RKH DERKH RKH A3 preferred P 1° Anchor KYRHFA deleteriousA11 preferred YFW P 1° Anchor KRYH deleterious A G A24 preferred YFW YFW1° Anchor 9-mer FLIW deleterious G AQN A24 preferred P 1° Anchor 10-merFLIW deleterious A QN DEA A3101 preferred YFW AP 1° Anchor RKdeleterious DE DE A3301 preferred AYFW 1° Anchor RK deleterious A6801preferred YFW P 1° Anchor RK deleterious A B0702 preferred RHK PA 1°Anchor LMFWYAIV deleterious QN DE B3501 preferred FWY 1° Anchor LMFWYIVAdeleterious B51 preferred G FWY 1° Anchor LIVFWYAM deleterious DEQN GDEB5301 preferred LIVMFWY FWY 1° Anchor IMFWYALV deleterious RHKQN DEB5401 preferred ALIVM FWYAP 1° Anchor ATIVLMFWY deleterious QNDGE DEItalicized residues indicate less preferred or “tolerated” residues. Theinformation in this Table is specific for 9-mers unless otherwisespecified.

TABLE V V1-A1-9mers: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 Score SEQ ID 152 D LL L I L L S Y 2.500 19. 66 V A V S N P L R Y 2.500 20. 150 G V D L L L IL L 2.500 21. 78 L T D S R I A Q I 2.500 22. 102 V A L L I R L S Y 2.50023. 186 H I V A F A I Y Y 2.500 24. 172 S P E E R K E T F 2.250 25. 51 VM E S S V L L A 2.250 26. 200 L S I V H R F G K 1.500 27. 10 A T D L G LS I S 1.250 28. 21 V T M L S I F W F 1.250 29. 131 C T D T R I N S A1.250 30. 39 C L S H M F F I K 1.000 31. 114 Q V L H H S Y C Y 1.000 32.40 L S H M F F I K F 0.750 33. 112 H S Q V L H H S Y 0.750 34. 54 S S VL L A M A F 0.750 35. 123 H P D V M K L S C 0.625 36. 37 N A C L S H M FF 0.500 37. 56 V L L A M A F D R 0.500 38. 157 L L S Y V L I I R 0.50039. 120 Y C Y H P D V M K 0.400 40. 68 V S N P L R Y A M 0.300 41. 226 SP L M N P V I Y 0.250 42. 65 F V A V S N P L R 0.200 43. 85 Q I G V A SV I R 0.200 44. 197 L I S L S I V H R 0.200 45. 97 M L T P M V A L L0.200 46. 138 S A V G L T A M F 0.200 47. 182 T C V S H I V A F 0.20048. 169 S V A S P E E R K 0.200 49. 168 L S V A S P E E R 0.150 50. 198I S L S I V H R F 0.150 51. 24 L S I F W F N V R 0.150 52. 18 S T L V TM L S I 0.125 53. 99 T P M V A L L I R 0.125 54. 98 L T P M V A L L I0.125 55. 181 S T C V S H I V A 0.125 56. 147 S T V G V D L L L 0.12557. 224 L I S P L M N P V 0.100 58. 19 T L V T M L S I F 0.100 59. 57 LL A M A F D R F 0.100 60. 74 Y A M I L T D S R 0.100 61. 228 L M N P V IY S V 0.100 62. 158 L S Y V L I I R T 0.075 63. 89 A S V I R G L L M0.075 64. 184 V S H I V A F A I 0.075 65. 17 I S T L V T M L S 0.075 66.34 I S F N A C L S H 0.075 67. 77 I L T D S R I A Q 0.050 68. 9 S A T DL G L S I 0.050 69. 217 M I A N T Y L L I 0.050 70. 110 Y C H S Q V L HH 0.050 71. 185 S H I V A F A I Y 0.050 72. 191 A T Y Y I P L I S 0.05073. 235 S V K T K Q I R R 0.050 74. 222 Y L L I S P L M N 0.050 75. 130S C T D T R I N S 0.050 76. 20 L V T M L S I F W 0.050 77. 14 G L S I ST L V T 0.050 78. 38 A C L S H M F F I 0.050 79. 23 M L S I F W F N V0.050 80. 194 Y I P L I S L S I 0.050 81. 7 M L S A T D L G L 0.050 82.95 L L M L T P M V A 0.050 83. 148 T V G V D L L L I 0.050 84. 229 M N PV I Y S V K 0.050 85. 156 I L L S Y V L I I 0.050 86. 139 A V G L T A MF S 0.050 87. 218 I A N T Y L L I S 0.050 88. 243 R A V I K I L H S0.050 89. 178 E T F S T C V S H 0.050 90. 176 R K E T F S T C V 0.04591. 31 V R E I S F N A C 0.045 92. 15 L S I S T L V T M 0.030 93. 208 KQ A P A Y V H T 0.030 94. 53 E S S V L L A M A 0.030 95. 225 I S P L M NP V I 0.030 96. 118 H S Y C Y H P D V 0.030 97. 215 H T M I A N T Y L0.025 98. 142 L T A M F S T V G 0.025 99. 49 F T V M E S S V L 0.025100. 220 N T Y L L I S P L 0.025 101. 42 H M F F I K F F T 0.025 102. 28W F N V R E I S F 0.025 103. 59 A M A F D R F V A 0.025 104. 214 V H T MI A N T Y 0.025 105. 36 F N A C L S H M F 0.025 106. 121 C Y H P D V M KL 0.025 107. 213 Y V H T M I A N T 0.020 108. 143 T A M F S T V G V0.020 109. 50 T V M E S S V L L 0.020 110. 83 I A Q I G V A S V 0.020111. 161 V L I I R T V L S 0.020 112. 231 P V I Y S V K T K 0.020 113.60 M A F D R F V A V 0.020 114. 183 C V S H I V A F A 0.020 115. 154 L LI L L S Y V L 0.020 116. 187 I V A F A I Y Y I 0.020 117. 244 A V I K IL H S K 0.020 118.

TABLE V V1B-A1-9mers: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 Score SEQ ID 23 G LE A F H T W I 0.900 119. 59 L H E P M Y Y F L 0.900 120. 31 I S I P F CF L S 0.750 121. 8 N I T S T S I I F 0.500 122. 43 L L G N S L I L F0.500 123. 57 P S L H E P M Y Y 0.375 124. 56 Q P S L H E P M Y 0.250125. 19 T G V P G L E A F 0.250 126. 58 S L H E P M Y Y F 0.200 127. 9 IT S T S I I F L 0.125 128. 18 L T G V P G L E A 0.125 129. 11 S T S I IF L L T 0.125 130. 3 T S T L Q N I T S 0.075 131. 10 T S T S I I F L L0.075 132. 38 L S V T A L L G N 0.075 133. 12 T S I I F L L T G 0.075134. 37 F L S V T A L L G 0.050 135. 32 S I P F C F L S V 0.050 136. 25E A F H T W I S I 0.050 137. 48 L I L F A T I T Q 0.050 138. 42 A L L GN S L I L 0.050 139. 46 N S L I L F A T I 0.030 140. 27 F H T W I S I PF 0.025 141. 4 S T L Q N I T S T 0.025 142. 54 I T Q P S L H E P 0.025143. 40 V T A L L G N S L 0.025 144. 2 I T S T L Q N I T 0.025 145. 52 AT I T Q P S L H 0.025 146. 29 T W I S I P F C F 0.025 147. 20 G V P G LE A F H 0.020 148. 51 F A T I T Q P S L 0.020 149. 16 F L L T G V P G L0.020 150. 61 E P M Y Y F L S M 0.013 151. 21 V P G L E A F H T 0.013152. 45 G N S L I L F A T 0.013 153. 44 L G N S L I L F A 0.013 154. 13S I I F L L T G V 0.010 155. 1 F I T S T L Q N I 0.010 156. 35 F C F L SV T A L 0.010 157. 47 S L I L F A T I T 0.010 158. 41 T A L L G N S L I0.010 159. 39 S V T A L L G N S 0.010 160. 30 W I S I P F C F L 0.010161. 5 T L Q N I T S T S 0.010 162. 53 T I T Q P S L H E 0.005 163. 28 HT W I S I P F C 0.005 164. 60 H E P M Y Y F L S 0.003 165. 33 I P F C FL S V T 0.003 166. 7 Q N I T S T S I I 0.003 167. 55 T Q P S L H E P M0.002 168. 6 L Q N I T S T S I 0.002 169. 14 I I F L L T G V P 0.001170. 36 C F L S V T A L L 0.001 171. 49 I L F A T I T Q P 0.001 172. 15I F L L T G V P G 0.001 173. 17 L L T G V P G L E 0.001 174. 50 L F A TI T Q P S 0.001 175. 62 P M Y Y F L S M L 0.001 176. 24 L E A F H T W IS 0.001 177. 22 P G L E A F H T W 0.000 178. 34 P F C F L S V T A 0.000179. 26 A F H T W I S I P 0.000 180. 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000

TABLE V V2-A1-9mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 8 L T SP L M N P V 0.250 181. 1 M I A N T Y L L T 0.050 182. 2 I A N T Y L L TS 0.050 183. 6 Y L L T S P L M N 0.050 184. 9 T S P L M N P V I 0.030185. 4 N T Y L L T S P L 0.025 186. 7 L L T S P L M N P 0.005 187. 5 T YL L T S P L M 0.001 188. 3 A N T Y L L T S P 0.000 189.

TABLE VI V1-A1-10mers: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 Score SEQ ID 10 AT D L G L S I S T 6.250 190. 150 G V D L L L I L L S 2.500 191. 65 F V AV S N P L R Y 2.500 192. 101 M V A L L I R L S Y 2.500 193. 51 V M E S SV L L A M 2.250 194. 225 I S P L M N P V I Y 1.500 195. 184 V S H I V AF A I Y 1.500 196. 78 L T D S R I A Q I G 1.250 197. 98 L T P M V A L LI R 1.250 198. 131 C T D T R I N S A V 1.250 199. 38 A C L S H M F F I K1.000 200. 228 L M N P V I Y S V K 1.000 201. 199 S L S I V H R F G K1.000 202. 53 E S S V L L A M A F 0.750 203. 39 C L S H M F F I K F0.500 204. 55 S V L L A M A F D R 0.500 205. 156 I L L S Y V L I I R0.500 206. 20 L V T M L S I F W F 0.500 207. 213 Y V H T M I A N T Y0.500 208. 97 M L T P M V A L L I 0.500 209. 181 S T C V S H I V A F0.500 210. 68 V S N P L R Y A M I 0.300 211. 168 L S V A S P E E R K0.300 212. 137 N S A V G L T A M F 0.300 213. 18 S T L V T M L S I F0.250 214. 172 S P E E R K E T F S 0.225 215. 243 R A V I K I L H S K0.200 216. 224 L I S P L M N P V I 0.200 217. 40 L S H M F F I K F F0.150 218. 171 A S P E E R K E T F 0.150 219. 113 S Q V L H H S Y C Y0.150 220. 185 S H I V A F A I Y Y 0.125 221. 151 V D L L L I L L S Y0.125 222. 36 F N A C L S H M F F 0.125 223. 123 H P D V M K L S C T0.125 224. 147 S T V G V D L L L I 0.125 225. 170 V A S P E E R K E T0.100 226. 56 V L L A M A F D R F 0.100 227. 167 V L S V A S P E E R0.100 228. 23 M L S I F W F N V R 0.100 229. 197 L I S L S I V H R F0.100 230. 31 V R E I S F N A C L 0.090 231. 234 Y S V K T K Q I R R0.075 232. 8 L S A T D L G L S I 0.075 233. 180 F S T C V S H I V A0.075 234. 146 F S T V G V D L L L 0.075 235. 17 I S T L V T M L S I0.075 236. 129 L S C T D T R I N S 0.075 237. 89 A S V I R G L L M L0.075 238. 204 H R F G K Q A P A Y 0.050 239. 94 G L L M L T P M V A0.050 240. 85 Q I G V A S V I R G 0.050 241. 88 V A S V I R G L L M0.050 242. 220 N T Y L L I S P L M 0.050 243. 183 C V S H I V A F A I0.050 244. 190 F A I Y Y I P L I S 0.050 245. 135 R I N S A V G L T A0.050 246. 76 M I L T D S R I A Q 0.050 247. 37 N A C L S H M F F I0.050 248. 215 H T M I A N T Y L L 0.050 249. 217 M I A N T Y L L I S0.050 250. 155 L I L L S Y V L I I 0.050 251. 188 V A F A I Y Y I P L0.050 252. 49 F T V M E S S V L L 0.050 253. 148 T V G V D L L L I L0.050 254. 50 T V M E S S V L L A 0.050 255. 191 A I Y Y I P L I S L0.050 256. 16 S I S T L V T M L S 0.050 257. 33 E I S F N A C L S H0.050 258. 19 T L V T M L S I F W 0.050 259. 142 L T A M F S T V G V0.050 260. 120 Y C Y H P D V M K L 0.050 261. 138 S A V G L T A M F S0.050 262. 139 A V G L T A M F S T 0.050 263. 230 N P V I Y S V K T K0.050 264. 161 V L I I R T V L S V 0.050 265. 58 L A M A F D R F V A0.050 266. 157 L L S Y V L I I R T 0.050 267. 176 R K E T F S T C V S0.045 268. 84 A Q I G V A S V I R 0.030 269. 108 L S Y C H S Q V L H0.030 270. 178 E T F S T C V S H I 0.025 271. 6 S M L S A T D L G L0.025 272. 111 C H S Q V L H H S Y 0.025 273. 21 V T M L S I F W F N0.025 274. 27 F W F N V R E I S F 0.025 275. 193 Y Y I P L I S L S I0.025 276. 42 H M F F I K F F T V 0.025 277. 216 T M I A N T Y L L I0.025 278. 22 T M L S I F W F N V 0.025 279. 14 G L S I S T L V T M0.020 280. 119 S Y C Y H P D V M K 0.020 281. 103 A L L I R L S Y C H0.020 282. 182 T C V S H I V A F A 0.020 283. 60 M A F D R F V A V S0.020 284. 153 L L L I L L S Y V L 0.020 285. 154 L L I L L S Y V L I0.020 286. 160 Y V L I I R T V L S 0.020 287. 82 R I A Q I G V A S V0.020 288. 67 A V S N P L R Y A M 0.020 289.

TABLE VI V1B-A1-10mers: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 Score SEQ ID 59L H E P M Y Y F L S 2.250 290. 23 G L E A F H T W I S 0.900 291. 31 I SI P F C F L S V 0.750 292. 56 Q P S L H E P M Y Y 0.625 293. 42 A L L GN S L I L F 0.500 294. 54 I T Q P S L H E P M 0.250 295. 18 L T G V P GL E A F 0.250 296. 55 T Q P S L H E P M Y 0.150 297. 2 I T S T L Q N I TS 0.125 298. 7 Q N I T S T S I I F 0.125 299. 28 H T W I S I P F C F0.125 300. 9 I T S T S I I F L L 0.125 301. 11 S T S I I F L L T G 0.125302. 10 T S T S I I F L L T 0.075 303. 19 T G V P G L E A F H 0.050 304.47 S L I L F A T I T Q 0.050 305. 37 F L S V T A L L G N 0.050 306. 20 GV P G L E A F H T 0.050 307. 30 W I S I P F C F L S 0.050 308. 8 N I T ST S I I F L 0.050 309. 43 L L G N S L I L F A 0.050 310. 41 T A L L G NS L I L 0.050 311. 17 L L T G V P G L E A 0.050 312. 57 P S L H E P M YY F 0.030 313. 40 V T A L L G N S L I 0.025 314. 4 S T L Q N I T S T S0.025 315. 26 A F H T W I S I P F 0.025 316. 58 S L H E P M Y Y F L0.020 317. 35 F C F L S V T A L L 0.020 318. 14 I I F L L T G V P G0.020 319. 46 N S L I L F A T I T 0.015 320. 3 T S T L Q N I T S T 0.015321. 38 L S V T A L L G N S 0.015 322. 12 T S I I F L L T G V 0.015 323.52 A T I T Q P S L H E 0.013 324. 44 L G N S L I L F A T 0.013 325. 1 FI T S T L Q N I T 0.010 326. 5 T L Q N I T S T S I 0.010 327. 32 S I P FC F L S V T 0.010 328. 39 S V T A L L G N S L 0.010 329. 49 I L F A T IT Q P S 0.010 330. 51 F A T I T Q P S L H 0.010 331. 45 G N S L I L F AT I 0.005 332. 33 I P F C F L S V T A 0.005 333. 60 H E P M Y Y F L S M0.003 334. 24 L E A F H T W I S I 0.003 335. 36 C F L S V T A L L G0.003 336. 21 V P G L E A F H T W 0.003 337. 61 E P M Y Y F L S M L0.003 338. 62 P M Y Y F L S M L S 0.003 339. 6 L Q N I T S T S I I 0.002340. 27 F H T W I S I P F C 0.001 341. 16 F L L T G V P G L E 0.001 342.13 S I I F L L T G V P 0.001 343. 50 L F A T I T Q P S L 0.001 344. 25 EA F H T W I S I P 0.001 345. 48 L I L F A T I T Q P 0.001 346. 15 I F LL T G V P G L 0.001 347. 53 T I T Q P S L H E P 0.001 348. 29 T W I S IP F C F L 0.001 349. 22 P G L E A F H T W I 0.000 350. 34 P F C F L S VT A L 0.000 351. 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.0000 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.0000 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.0000 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.0000 0.000 0 0.000 0 0.000 0 0.000

TABLE VI V2-A1-10mers SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 10 T S P L MN P V I Y 1.500 352. 9 L T S P L M N P V I 0.500 353. 5 N T Y L L T S PL M 0.050 354. 2 M I A N T Y L L T S 0.050 355. 1 T M I A N T Y L L T0.025 356. 8 L L T S P L M N P V 0.010 357. 7 Y L L T S P L M N P 0.005358. 6 T Y L L T S P L M N 0.003 359. 4 A N T Y L L T S P L 0.003 360. 3I A N T Y L L T S P 0.001 361.

TABLE VII V1-A2-9mers: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 Score SEQ ID 153 LL L I L L S Y V 5534.148 362. 23 M L S I F W F N V 4430.156 363. 94 G LL M L T P M V 257.342 364. 103 A L L I R L S Y C 232.527 365. 96 L M L TP M V A L 223.203 366. 228 L M N P V I Y S V 196.407 367. 141 G L T A MF S T V 132.149 368. 97 M L T P M V A L L 83.527 369. 107 R L S Y C H SQ V 69.552 370. 156 I L L S Y V L I I 61.882 371. 60 M A F D R F V A V47.333 372. 224 L I S P L M N P V 37.393 373. 162 L I I R T V L S V37.393 374. 128 K L S C T D T R I 36.515 375. 7 M L S A T D L G L 36.316376. 50 T V M E S S V L L 28.356 377. 58 L A M A F D R F V 25.398 378.42 H M F F I K F F T 21.598 379. 187 I V A F A I Y Y I 19.631 380. 38 AC L S H M F F I 18.488 381. 22 T M L S I F W F N 15.607 382. 216 T M I AN T Y L L 15.428 383. 154 L L I L L S Y V L 14.890 384. 155 L I L L S YV L I 13.535 385. 160 Y V L I I R T V L 13.044 386. 95 L L M L T P M V A12.812 387. 59 A M A F D R F V A 8.532 388. 75 A M I L T D S R I 7.535389. 213 Y V H T M I A N T 6.899 390. 16 S I S T L V T M L 6.756 391.194 Y I P L I S L S I 6.599 392. 183 C V S H I V A F A 5.499 393. 90 S VI R G L L M L 4.299 394. 140 V G L T A M F S T 4.082 395. 208 K Q A P AY V H T 3.967 396. 83 I A Q I G V A S V 3.777 397. 12 D L G L S I S T L3.685 398. 217 M I A N T Y L L I 3.658 399. 143 T A M F S T V G V 3.574400. 43 M F F I K F F T V 3.348 401. 14 G L S I S T L V T 3.055 402. 13L G L S I S T L V 2.856 403. 202 I V H R F G K Q A 2.808 404. 113 S Q VL H H S Y C 2.770 405. 195 I P L I S L S I V 2.693 406. 220 N T Y L L IS P L 2.184 407. 148 T V G V D L L L I 2.100 408. 150 G V D L L L I L L1.720 409. 32 R E I S F N A C L 1.578 410. 190 F A I Y Y I P L I 1.533411. 222 Y L L I S P L M N 1.268 8912 18 S T L V T M L S I 1.233 8913 67A V S N P L R Y A 1.100 412. 115 V L H H S Y C Y H 1.045 413. 149 V G VD L L L I L 0.917 414. 51 V M E S S V L L A 0.898 415. 5 L S M L S A T DL 0.877 416. 87 G V A S V I R G L 0.860 417. 180 F S T C V S H I V 0.856418. 30 N V R E I S F N A 0.786 419. 100 P M V A L L I R L 0.781 420.146 F S T V G V D L L 0.723 421. 184 V S H I V A F A I 0.671 422. 158 LS Y V L I I R T 0.609 423. 9 S A T D L G L S I 0.594 424. 49 F T V M E SS V L 0.560 425. 56 V L L A M A F D R 0.544 426. 21 V T M L S I F W F0.478 427. 84 A Q I G V A S V I 0.434 428. 206 F G K Q A P A Y V 0.402429. 52 M E S S V L L A M 0.378 430. 76 M I L T D S R I A 0.352 431. 126V M K L S C T D T 0.320 432. 108 L S Y C H S Q V L 0.311 433. 135 R I NS A V G L T 0.306 434. 91 V I R G L L M L T 0.304 435. 147 S T V G V D LL L 0.297 436. 93 R G L L M L T P M 0.276 437. 240 Q I R R A V I K I0.251 438. 98 L T P M V A L L I 0.246 439. 78 L T D S R I A Q I 0.227440. 48 F F T V M E S S V 0.222 441. 70 N P L R Y A M I L 0.212 442. 215H T M I A N T Y L 0.205 443. 3 Y F L S M L S A T 0.203 444. 171 A S P EE R K E T 0.199 445. 209 Q A P A Y V H T M 0.159 446. 15 L S I S T L V TM 0.127 447. 104 L L I R L S Y C H 0.127 448. 161 V L I I R T V L S0.127 449. 57 L L A M A F D R F 0.118 450. 77 I L T D S R I A Q 0.104451. 69 S N P L R Y A M I 0.102 452. 6 S M L S A T D L G 0.098 453. 132T D T R I N S A V 0.097 454. 163 I I R T V L S V A 0.083 455. 199 S L SI V H R F G 0.082 456. 227 P L M N P V I Y S 0.077 457. 137 N S A V G LT A M 0.075 458. 19 T L V T M L S I F 0.070 459.

TABLE VII V1B-A2-9mers: 238P1B2 SEQ Pos 1 2 4 5 6 7 8 9 Score ID 16 F LL T G V P G L 836.253 460. 30 W I S I P F C F L 141.197 461. 42 A L L GN S L I L 32.407 462. 13 S I I F L L T G V 21.996 463. 32 S I P F C F LS V 18.170 464. 1 F I T S T L Q N I 15.177 465. 23 G L E A F H T W I13.955 466. 47 S L I L F A T I T 11.610 467. 62 P M Y Y F L S M L 9.493468. 9 I T S T S I I F L 6.381 469. 35 F C F L S V T A L 5.459 470. 58 SL H E P M Y Y F 3.865 471. 10 T S T S I I F L L 1.860 472. 6 L Q N I T ST S I 1.798 473. 51 F A T I T Q P S L 1.365 474. 33 I P F C F L S V T1.096 475. 4 S T L Q N I T S T 0.881 476. 44 L G N S L I L F A 0.697477. 45 G N S L I L F A T 0.649 478. 41 T A L L G N S L I 0.536 479. 40V T A L L G N S L 0.504 480. 21 V P G L E A F H T 0.480 481. 46 N S L IL F A T I 0.479 482. 37 F L S V T A L L G 0.343 483. 43 L L G N S L I LF 0.291 484. 55 T Q P S L H E P M 0.247 485. 28 H T W I S I P F C 0.246486. 49 I L F A T I T Q P 0.216 487. 11 S T S I I F L L T 0.197 488. 18L T G V P G L E A 0.117 489. 5 T L Q N I T S T S 0.075 490. 2 I T S T LQ N I T 0.072 491. 25 E A F H T W I S I 0.068 492. 36 C F L S V T A L L0.055 493. 20 G V P G L E A F H 0.036 494. 7 Q N I T S T S I I 0.028495. 31 I S I P F C F L S 0.018 496. 61 E P M Y Y F L S M 0.017 497. 59L H E P M Y Y F L 0.013 498. 48 L I L F A T I T Q 0.013 499. 24 L E A FH T W I S 0.008 500. 12 T S I I F L L T G 0.004 501. 8 N I T S T S I I F0.004 502. 17 L L T G V P G L E 0.003 503. 53 T I T Q P S L H E 0.002504. 39 S V T A L L G N S 0.002 505. 38 L S V T A L L G N 0.002 506. 52A T I T Q P S L H 0.001 507. 54 I T Q P S L H E P 0.001 508. 14 I I F LL T G V P 0.001 509. 19 T G V P G L E A F 0.001 510. 3 T S T L Q N I T S0.000 511. 56 Q P S L H E P M Y 0.000 512. 60 H E P M Y Y F L S 0.000513. 15 I F L L T G V P G 0.000 514. 22 P G L E A F H T W 0.000 515. 27F H T W I S I P F 0.000 516. 57 P S L H E P M Y Y 0.000 517. 50 L F A TI T Q P S 0.000 518. 34 P F C F L S V T A 0.000 519. 29 T W I S I P F CF 0.000 520. 26 A F H T W I S I P 0.000 521. 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000

TABLE VII V2-A2-9mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 8 L TS P L M N P V 3.777 522. 1 M I A N T Y L L T 2.613 523. 6 Y L L T S P LM N 1.268 524. 4 N T Y L L T S P L 0.949 525. 7 L L T S P L M N P 0.058526. 9 T S P L M N P V I 0.028 527. 2 I A N T Y L L T S 0.004 528. 5 T YL L T S P L M 0.003 529. 3 A N T Y L L T S P 0.000 530.

TABLE VIII V1-A2-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 22T M L S I F W F N V 6963.743 531. 57 L L A M A F D R F V 494.237 532. 95L L M L T P M V A L 309.050 533. 223 L L I S P L M N P V 271.948 534.161 V L I I R T V L S V 271.948 535. 152 D L L L I L L S Y V 244.154536. 96 L M L T P M V A L L 223.203 537. 77 I L T D S R I A Q I 167.248538. 4 F L S M L S A T D L 98.267 539. 59 A M A F D R F V A V 95.441540. 42 H M F F I K F F T V 69.637 541. 144 A M F S T V G V D L 57.085542. 6 S M L S A T D L G L 57.085 543. 153 L L L I L L S Y V L 55.091544. 194 Y I P L I S L S I V 41.484 545. 157 L L S Y V L I I R T 29.137546. 154 L L I L L S Y V L I 26.604 547. 82 R I A Q I G V A S V 21.996548. 191 A I Y Y I P L I S L 21.619 549. 97 M L T P M V A L L I 17.736550. 50 T V M E S S V L L A 15.167 551. 227 P L M N P V I Y S V 13.022552. 14 G L S I S T L V T M 11.426 553. 216 T M I A N T Y L L I 11.302554. 37 N A C L S H M F F I 10.631 555. 107 R L S Y C H S Q V L 8.759556. 139 A V G L T A M F S T 8.698 557. 239 K Q I R R A V I K I 8.515558. 155 L I L L S Y V L I I 8.509 559. 232 V I Y S V K T K Q I 7.804560. 94 G L L M L T P M V A 7.536 561. 102 V A L L I R L S Y C 5.490562. 140 V G L T A M F S T V 5.426 563. 183 C V S H I V A F A I 5.295564. 12 D L G L S I S T L V 5.216 565. 120 Y C Y H P D V M K L 4.721566. 208 K Q A P A Y V H T M 4.055 567. 188 V A F A I Y Y I P L 2.799568. 201 S I V H R F G K Q A 2.596 569. 74 Y A M I L T D S R I 2.466570. 25 S I F W F N V R E I 2.442 571. 149 V G V D L L L I L L 2.236572. 148 T V G V D L L L I L 1.763 573. 93 R G L L M L T P M V 1.680574. 142 L T A M F S T V G V 1.642 575. 90 S V I R G L L M L T 1.500576. 49 F T V M E S S V L L 1.365 577. 99 T P M V A L L I R L 1.187 578.158 L S Y V L I I R T V 1.136 579. 162 L I I R T V L S V A 1.095 580. 58L A M A F D R F V A 1.032 581. 224 L I S P L M N P V I 1.000 582. 51 V ME S S V L L A M 0.898 583. 29 F N V R E I S F N A 0.865 584. 20 L V T ML S I F W F 0.813 585. 135 R I N S A V G L T A 0.683 586. 146 F S T V GV D L L L 0.641 587. 47 K F F T V M E S S V 0.625 588. 186 H I V A F A IY Y I 0.617 589. 41 S H M F F I K F F T 0.611 590. 222 Y L L I S P L M NP 0.583 591. 15 L S I S T L V T M L 0.545 592. 39 C L S H M F F I K F0.538 593. 21 V T M L S I F W F N 0.510 594. 34 I S F N A C L S H M0.469 595. 56 V L L A M A F D R F 0.436 596. 67 A V S N P L R Y A M0.435 597. 70 N P L R Y A M I L T 0.414 598. 182 T C V S H I V A F A0.410 599. 19 T L V T M L S I F W 0.410 600. 131 C T D T R I N S A V0.386 601. 52 M E S S V L L A M A 0.378 602. 147 S T V G V D L L L I0.333 603. 219 A N T Y L L I S P L 0.321 604. 89 A S V I R G L L M L0.321 605. 130 S C T D T R I N S A 0.306 606. 66 V A V S N P L R Y A0.297 607. 75 A M I L T D S R I A 0.294 608. 103 A L L I R L S Y C H0.276 609. 17 I S T L V T M L S I 0.266 610. 205 R F G K Q A P A Y V0.266 611. 30 N V R E I S F N A C 0.257 612. 11 T D L G L S I S T L0.252 613. 87 G V A S V I R G L L 0.243 614. 220 N T Y L L I S P L M0.221 615. 240 Q I R R A V I K I L 0.211 616. 114 Q V L H H S Y C Y H0.199 617. 104 L L I R L S Y C H S 0.190 618. 125 D V M K L S C T D T0.181 619. 170 V A S P E E R K E T 0.176 620. 68 V S N P L R Y A M I0.174 621. 209 Q A P A Y V H T M I 0.145 622. 214 V H T M I A N T Y L0.139 623. 136 I N S A V G L T A M 0.127 624. 13 L G L S I S T L V T0.125 625. 88 V A S V I R G L L M 0.117 626. 141 G L T A M F S T V G0.116 627. 8 L S A T D L G L S I 0.116 628. 160 Y V L I I R T V L S0.111 629. 86 I G V A S V I R G L 0.109 630.

TABLE VIII V1B-A2-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID58 S L H E P M Y Y F L 722.583 631. 43 L L G N S L I L F A 106.837 632.8 N I T S T S I I F L 37.157 633. 5 T L Q N I T S T S I 10.433 634. 17 LL T G V P G L E A 8.446 635. 9 I T S T S I I F L L 6.729 636. 20 G V P GL E A F H T 3.782 637. 32 S I P F C F L S V T 3.672 638. 35 F C E L S VT A L L 2.373 639. 1 F I T S T L Q N I T 1.932 640. 39 S V T A L L G N SL 1.869 641. 31 I S I P F C F L S V 1.466 642. 44 L G N S L I L F A T1.103 643. 12 T S I I F L L T G V 1.044 644. 30 W I S I P F C F L S1.039 645. 37 F L S V T A L L G N 0.788 646. 6 L Q N I T S T S I I 0.737647. 42 A L L G N S L I L F 0.634 648. 24 L E A F H T W I S I 0.586 649.22 P G L E A F H T W I 0.475 650. 49 I L F A T I T Q P S 0.469 651. 41 TA L L G N S L I L 0.450 652. 61 E P M Y Y F L S M L 0.338 653. 46 N S LI L F A T I T 0.280 654. 40 V T A L L G N S L I 0.246 655. 15 I F L L TG V P G L 0.215 656. 33 I P F C F L S V T A 0.204 657. 27 F H T W I S IP F C 0.201 658. 45 G N S L I L F A T I 0.129 659. 3 T S T L Q N I T S T0.112 660. 10 T S T S I I F L L T 0.092 661. 14 I I F L L T G V P G0.064 662. 54 I T Q P S L H E P M 0.057 663. 16 F L L T G V P G L E0.033 664. 29 T W I S I P F C F L 0.031 665. 48 L I L F A T I T Q P0.030 666. 50 L F A T I T Q P S L 0.025 667. 47 S L I L F A T I T Q0.015 668. 23 G L E A F H T W I S 0.015 669. 11 S T S I I F L L T G0.009 670. 55 T Q P S L H E P M Y 0.008 671. 60 H E P M Y Y F L S M0.006 672. 51 F A T I T Q P S L H 0.005 673. 53 T I T Q P S L H E P0.005 674. 4 S T L Q N I T S T S 0.004 675. 62 P M Y Y F L S M L S 0.004676. 19 T G V P G L E A F H 0.003 677. 56 Q P S L H E P M Y Y 0.003 678.18 L T G V P G L E A F 0.002 679. 2 I T S T L Q N I T S 0.002 680. 28 HT W I S I P F C F 0.002 681. 21 V P G L E A F H T W 0.002 682. 34 P F CF L S V T A L 0.001 683. 57 P S L H E P M Y Y F 0.001 684. 38 L S V T AL L G N S 0.000 685. 52 A T I T Q P S L H E 0.000 686. 7 Q N I T S T S II F 0.000 687. 36 C F L S V T A L L G 0.000 688. 13 S I I F L L T G V P0.000 689. 25 E A F H T W I S I P 0.000 690. 26 A F H T W I S I P F0.000 691. 59 L H E P M Y Y F L S 0.000 692. 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000

TABLE VIII V2-A2-10mers SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 8 L L T S PL M N P V 271.948 693. 1 T M I A N T Y L L T 8.073 694. 7 Y L L T S P LM N P 0.583 695. 5 N T Y L L T S P L M 0.221 696. 4 A N T Y L L T S P L0.139 697. 9 L T S P L M N P V I 0.101 698. 2 M I A N T Y L L T S 0.040699. 3 I A N T Y L L T S P 0.001 700. 10 T S P L M N P V I Y 0.000 701.6 T Y L L T S P L M N 0.000 702.

TABLE IX V1-A3-9-mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 39 C LS H M F F I K 180.000 703. 157 L L S Y V L I I R 18.000 704. 56 V L L AN A F D R 18.000 705. 156 I L L S Y V L I I 16.200 706. 152 D L L L I LL S Y 8.100 707. 244 A V I K I L H S K 6.750 708. 57 L L A M A F D R F6.000 709. 19 T L V T M L S I F 4.500 710. 186 H I V A F A I Y Y 3.600711. 169 S V A S P E E R K 3.000 712. 216 T M I A N T Y L L 2.700 713.97 M L T P M V A L L 2.700 714. 239 K Q I R R A V I K 2.700 715. 154 L LI L L S Y V L 2.700 716. 42 H M F F I K F F T 2.250 717. 228 L M N P V IY S V 2.025 718. 96 L M L T P M V A L 2.025 719. 141 G L T A M F S T V1.800 720. 23 M L S I F W F N V 1.800 721. 128 K L S C T D T R I 1.800722. 114 Q V L H H S Y C Y 1.800 723. 120 Y C Y H P D V M K 1.500 724.51 V M E S S V L L A 1.200 725. 7 M L S A T D L G L 1.200 726. 104 L L IR L S Y C H 0.900 727. 94 G L L M L T P M V 0.900 728. 75 A M I L T D SR I 0.900 729. 235 S V K T K Q I R R 0.800 730. 21 V T M L S I F W F0.675 731. 95 L L M L T P M V A 0.600 732. 197 L I S L S I V H R 0.600733. 59 A M A F D R F V A 0.600 734. 14 G L S I S T L V T 0.600 735. 150G V D L L L I L L 0.540 736. 103 A L L I R L S Y C 0.450 737. 153 L L LI L L S Y V 0.450 738. 200 L S I V H R F G K 0.450 739. 231 P V I Y S VK T K 0.450 740. 22 T M L S I F W F N 0.405 741. 85 Q I G V A S V I R0.400 742. 65 F V A V S N P L R 0.400 743. 240 Q I R R A V I K I 0.360744. 12 D L G L S I S T L 0.270 745. 100 P M V A L L I R L 0.270 746. 24L S I F W F N V R 0.270 747. 90 S V I R G L L M L 0.270 748. 187 I V A FA I Y Y I 0.270 749. 220 N T Y L L I S P L 0.225 750. 147 S T V G V D LL L 0.203 751. 107 R L S Y C H S Q V 0.200 752. 115 V L H H S Y C Y H0.200 753. 194 Y I P L I S L S I 0.180 754. 16 S I S T L V T M L 0.180755. 148 T V G V D L L L I 0.180 756. 162 L I I R T V L S V 0.180 757.40 L S H M F F I K F 0.180 758. 99 T P M V A L L I R 0.180 759. 102 V AL L I R L S Y 0.180 760. 50 T V M E S S V L L 0.135 761. 30 N V R E I SF N A 0.135 762. 160 Y V L I I R T V L 0.135 763. 223 L L I S P L M N P0.135 764. 18 S T L V T M L S I 0.135 765. 66 V A V S N P L R Y 0.120766. 217 M I A N T Y L L I 0.120 767. 126 V M K L S C T D T 0.100 768.183 C V S H I V A F A 0.090 769. 98 L T P M V A L L I 0.090 770. 144 A MF S T V G V D 0.090 771. 155 L I L L S Y V L I 0.090 772. 198 I S L S IV H R F 0.068 773. 84 A Q I G V A S V I 0.061 774. 229 M N P V I Y S V K0.060 775. 191 A I Y Y I P L I S 0.060 776. 196 P L I S L S I V H 0.060777. 161 V L I I R T V L S 0.060 778. 74 Y A M I L T D S R 0.060 779.222 Y L L I S P L M N 0.060 780. 226 S P L M N P V I Y 0.060 781. 227 PL M N P V I Y S 0.054 782. 70 N P L R Y A M I L 0.054 783. 163 I I R T VL S V A 0.045 784. 49 F T V M E S S V L 0.045 785. 215 H T M I A N T Y L0.045 786. 182 T C V S H I V A F 0.045 787. 91 V I R G L L M L T 0.045788. 138 S A V G L T A M F 0.045 789. 78 L T D S R I A Q I 0.045 790.224 L I S P L M N P V 0.045 791. 87 G V A S V I R G L 0.041 792. 190 F AI Y Y I P L I 0.041 793. 38 A C L S H M F F I 0.041 794. 37 N A C L S HM F F 0.040 795. 20 L V T M L S I F W 0.040 796. 77 I L T D S R I A Q0.040 797. 234 Y S V K T K Q I R 0.030 798. 25 S I F W F N V R E 0.030799. 6 S M L S A T D L G 0.030 800. 202 I V H R F G K Q A 0.030 801. 168L S V A S P E E R 0.030 802.

TABLE IX V1B-A3-9mers: 238P1B2 SEQ ID Pos 1 2 3 4 5 6 7 8 9 Score 803.58 S L H E P M Y Y F 20.250 804. 43 L L G N S L I L F 6.000 805. 23 G LE A F H T W I 5.400 806. 42 A L L G N S L I L 2.700 807. 16 F L L T G VP G L 2.700 808. 62 P M Y Y F L S M L 1.350 809. 47 S L I L F A T I T0.450 810. 8 N I T S T S I I F 0.400 811. 30 W I S I P F C F L 0.270812. 49 I L F A T I T Q P 0.150 813. 32 S I P F C F L S V 0.120 814. 9 IT S T S I I F L 0.090 815. 20 G V P G L E A F H 0.090 816. 1 F I T S T LQ N I 0.090 817. 35 F C F L S V T A L 0.090 818. 28 H T W I S I P F C0.075 819. 5 T L Q N I T S T S 0.060 820. 11 S T S I I F L L T 0.045821. 13 S I I F L L T G V 0.045 822. 37 F L S V T A L L G 0.040 823. 56Q P S L H E P M Y 0.040 824. 18 L T G V P G L E A 0.030 825. 40 V T A LL G N S L 0.030 826. 33 I P F C F L S V T 0.022 827. 10 T S T S I I F LL 0.020 828. 6 L Q N I T S T S I 0.018 829. 25 E A F H T W I S I 0.018830. 61 E P M Y Y F L S M 0.016 831. 52 A T I T Q P S L H 0.015 832. 29T W I S I P F C F 0.013 833. 17 L L T G V P G L E 0.013 834. 46 N S L IL F A T I 0.013 835. 4 S T L Q N I T S T 0.011 836. 41 T A L L G N S L I0.009 837. 19 T G V P G L E A F 0.007 838. 27 F H T W I S I P F 0.006839. 57 P S L H E P M Y Y 0.006 840. 51 F A T I T Q P S L 0.006 841. 53T I T Q P S L H E 0.006 842. 48 L I L F A T I T Q 0.006 843. 55 T Q P SL H E P M 0.006 844. 2 I T S T L Q N I T 0.005 845. 45 G N S L I L F A T0.004 846. 31 I S I P F C F L S 0.004 847. 21 V P G L E A F H T 0.003848. 14 I I F L L T G V P 0.003 849. 59 L H E P M Y Y F L 0.003 850. 54I T Q P S L H E P 0.002 851. 7 Q N I T S T S I I 0.002 852. 39 S V T A LL G N S 0.002 853. 36 C F L S V T A L L 0.001 854. 12 T S I I F L L T G0.001 855. 60 H E P M Y Y F L S 0.001 856. 44 L G N S L I L F A 0.001857. 38 L S V T A L L G N 0.000 858. 3 T S T L Q N I T S 0.000 859. 24 LE A F H T W I S 0.000 860. 22 P G L E A F H T W 0.000 861. 26 A F H T WI S I P 0.000 862. 50 L F A T I T Q P S 0.000 863. 15 I F L L T G V P G0.000 864. 34 P F C F L S V T A 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000

TABLE IX V2-A3-9mers-238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 4 N T YL L T S P L 0.150 865 7 L L T S P L M N P 0.090 866 6 Y L L T S P L M N0.060 867 8 L T S P L M N P V 0.022 868 1 M I A N T Y L L T 0.020 869 2I A N T Y L L T S 0.004 870 9 T S P L M N P V I 0.003 871 5 T Y L L T SP L M 0.000 872 3 A N T Y L L T S P 0.000 873

TABLE X V1-A3-10-mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 199S L S I V H R F G K 60.000 874 228 L M N P V I Y S V K 45.000 875 39 C LS H M F F I K F 36.000 876 23 M L S I F W F N V R 36.000 877 156 I L L SY V L I I R 27.000 878 42 H M F F I K F F T V 9.000 879 56 V L L A M A FD R F 9.000 880 144 A M F S T V G V D L 4.500 881 167 V L S V A S P E ER 4.000 882 126 V M K L S C T D T R 4.000 883 153 L L L I L L S Y V L2.700 884 38 A C L S H M F F I K 2.700 885 22 T M L S I F W F N V 2.700886 96 L M L T P M V A L L 2.700 887 97 M L T P M V A L L I 2.700 888 95L L M L T P M V A L 2.025 889 6 S M L S A T D L G L 1.800 890 94 G L L ML T P M V A 1.800 891 161 V L I I R T V L S V 1.800 892 216 T M I A N TY L L I 1.800 893 55 S V L L A M A F D R 1.800 894 155 L I L L S Y V L II 1.620 895 191 A I Y Y I P L I S L 1.350 896 101 M V A L L I R L S Y1.200 897 14 G L S I S T L V T M 0.900 898 51 V M E S S V L L A M 0.900899 197 L I S L S I V H R F 0.900 900 196 P L I S L S I V H R 0.900 90120 L V T M L S I F W F 0.900 902 103 A L L I R L S Y C H 0.900 903 77 IL T D S R I A Q I 0.900 904 154 L L I L L S Y V L I 0.900 905 65 F V A VS N P L R Y 0.800 906 243 R A V I K I L H S K 0.675 907 98 L T P M V A LL I R 0.600 908 4 F L S M L S A T D L 0.600 909 107 R L S Y C H S Q V L0.600 910 213 Y V H T M I A N T Y 0.600 911 19 T L V T M L S I F W 0.600912 59 A M A F D R F V A V 0.600 913 113 S Q V L H H S Y C Y 0.540 914239 K Q I R R A V I K I 0.486 915 223 L L I S P L M N P V 0.450 916 230N P V I Y S V K T K 0.450 917 186 H I V A F A I Y Y I 0.405 918 157 L LS Y V L I I R T 0.300 919 84 A Q I G V A S V I R 0.270 920 50 T V M E SS V L L A 0.270 921 183 C V S H I V A F A I 0.270 922 208 K Q A P A Y VH T M 0.243 923 18 S T L V T M L S I F 0.225 924 168 L S V A S P E E R K0.225 925 147 S T V G V D L L L I 0.203 926 227 P L M N P V I Y S V0.203 927 148 T V G V D L L L I L 0.180 928 120 Y C Y H P D V M K L0.180 929 115 V L H H S Y C Y H P 0.180 930 188 V A F A I Y Y I P L0.180 931 141 G L T A M F S T V G 0.180 932 181 S T C V S H I V A F0.150 933 232 V I Y S V K T K Q I 0.150 934 215 H T M I A N T Y L L0.135 935 152 D L L L I L L S Y V 0.135 936 222 Y L L I S P L M N P0.135 937 178 E T F S T C V S H I 0.135 938 30 N V R E I S F N A C 0.090939 12 D L G L S I S T L V 0.090 940 224 L I S P L M N P V I 0.090 941237 K T K Q I R R A V I 0.090 942 25 S I F W F N V R E I 0.090 943 87 GV A S V I R G L L 0.081 944 220 N T Y L L I S P L M 0.075 945 240 Q I RR A V I K I L 0.068 946 162 L I I R T V L S V A 0.068 947 135 R I N S AV G L T A 0.060 948 67 A V S N P L R Y A M 0.060 949 104 L L I R L S Y CH S 0.060 950 57 L L A M A F D R F V 0.060 951 234 Y S V K T K Q I R R0.060 952 184 V S H I V A F A I Y 0.060 953 82 R I A Q I G V A S V 0.060954 201 S I V H R F G K Q A 0.045 955 139 A V G L T A M F S T 0.045 95690 S V I R G L L M L T 0.045 957 49 F T V M E S S V L L 0.045 958 185 SH I V A F A I Y Y 0.036 959 217 M I A N T Y L L I S 0.036 960 150 G V DL L L I L L S 0.036 961 119 S Y C Y H P D V M K 0.030 962 194 Y I P L IS L S I V 0.030 963 114 Q V L H H S Y C Y H 0.030 964 75 A M I L T D S RI A 0.030 965 204 H R F G K Q A P A Y 0.030 966 37 N A C L S H M F F I0.027 967 99 T P M V A L L I R L 0.027 968 151 V D L L L I L L S Y 0.027969 45 F I K F F T V M E S 0.024 970 40 L S H M F F I K F F 0.022 971 21V T M L S I F W F N 0.020 972 238 T K Q I R R A V I K 0.020 973

TABLE X V1B-A3-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 42 AL L G N S L I L F 13.500 974 58 S L H E P M Y Y F L 2.700 975 28 H T W IS I P F C F 2.250 976 17 L L T G V P G L E A 0.900 977 43 L L G N S L IL F A 0.600 978 5 T L Q N I T S T S I 0.600 979 23 G L E A F H T W I S0.360 980 49 I L F A T I T Q P S 0.300 981 9 I T S T S I I F L L 0.203982 8 N I T S T S I I F L 0.180 983 18 L T G V P G L E A F 0.150 984 20G V P G L E A F H T 0.135 985 55 T Q P S L H E P M Y 0.120 986 56 Q P SL H E P M Y Y 0.080 987 39 S V T A L L G N S L 0.060 988 47 S L I L F AT I T Q 0.060 989 37 F L S V T A L L G N 0.060 990 32 S I P F C F L S VT 0.045 991 35 F C F L S V T A L L 0.045 992 62 P M Y Y F L S M L S0.040 993 30 W I S I P F C F L S 0.036 994 40 V T A L L G N S L I 0.030995 6 L Q N I T S T S I I 0.018 996 41 T A L L G N S L I L 0.018 997 54I T Q P S L H E P M 0.015 998 16 F L L T G V P G L E 0.013 999 31 I S IP F C F L S V 0.013 1000 61 E P M Y Y F L S M L 0.012 1001 7 Q N I T S TS I I F 0.012 1002 45 G N S L I L F A T I 0.011 1003 60 H E P M Y Y F LS M 0.011 1004 57 P S L H E P M Y Y F 0.010 1005 1 F I T S T L Q N I T0.010 1006 14 I I F L L T G V P G 0.010 1007 33 I P F C F L S V T A0.010 1008 11 S T S I I F L L T G 0.009 1009 26 A F H T W I S I P F0.006 1010 21 V P G L E A F H T W 0.006 1011 10 T S T S I I F L L T0.005 1012 52 A T I T Q P S L H E 0.005 1013 4 S T L Q N I T S T S 0.0051014 48 L I L F A T I T Q P 0.005 1015 29 T W I S I P F C F L 0.004 10162 I T S T L Q N I T S 0.004 1017 24 L E A F H T W I S I 0.004 1018 53 TI T Q P S L H E P 0.003 1019 15 I F L L T G V P G L 0.003 1020 46 N S LI L F A T I T 0.002 1021 12 T S I I F L L T G V 0.002 1022 51 F A T I TQ P S L H 0.002 1023 25 E A F H T W I S I P 0.001 1024 13 S I I F L L TG V P 0.001 1025 3 T S T L Q N I T S T 0.001 1026 44 L G N S L I L F A T0.001 1027 50 L F A T I T Q P S L 0.001 1028 59 L H E P M Y Y F L S0.001 1029 19 T G V P G L E A F H 0.000 1030 22 P G L E A F H T W I0.000 1031 27 F H T W I S I P F C 0.000 1032 34 P F C F L S V T A L0.000 1033 38 L S V T A L L G N S 0.000 1034 36 C F L S V T A L L G0.000 1035 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000

TABLE X V2-A3-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 1 T MI A N T Y L L T 0.300 1036 8 L L T S P L M N P V 0.300 1037 7 Y L L T SP L M N P 0.135 1038 5 N T Y L L T S P L M 0.050 1039 9 L T S P L M N PV I 0.045 1040 2 M I A N T Y L L T S 0.036 1041 10 T S P L M N P V I Y0.020 1042 4 A N T Y L L T S P L 0.001 1043 3 I A N T Y L L T S P 0.0001044 6 T Y L L T S P L M N 0.000 1045

TABLE XI V1-A11-9mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 244 AV I K I L H S K 3.000 1046 239 K Q I R R A V I K 2.700 1047 169 S V A SP E E R K 2.000 1048 39 C L S H M F F I K 1.200 1049 235 S V K T K Q I RR 0.800 1050 65 F V A V S N P L R 0.400 1051 120 Y C Y H P D V M K 0.4001052 56 V L L A M A F D R 0.360 1053 157 L L S Y V L I I R 0.160 1054 99T P M V A L L I R 0.160 1055 231 P V I Y S V K T K 0.150 1056 150 G V DL L L I L L 0.120 1057 200 L S I V H R F G K 0.090 1058 197 L I S L S IV H R 0.080 1059 74 Y A M I L T D S R 0.080 1060 85 Q I G V A S V I R0.080 1061 30 N V R E I S F N A 0.060 1062 21 V T M L S I F W F 0.0601063 114 Q V L H H S Y C Y 0.060 1064 90 S V I R G L L M L 0.060 1065148 T V G V D L L L I 0.040 1066 20 L V T M L S I F W 0.040 1067 187 I VA F A I Y Y I 0.040 1068 50 T V M E S S V L L 0.040 1069 229 M N P V I YS V K 0.040 1070 147 S T V G V D L L L 0.030 1071 18 S T L V T M L S I0.030 1072 160 Y V L I I R T V L 0.030 1073 215 H T M I A N T Y L 0.0201074 181 S T C V S H I V A 0.020 1075 220 N T Y L L I S P L 0.020 107698 L T P M V A L L I 0.020 1077 183 C V S H I V A F A 0.020 1078 94 G LL M L T P M V 0.018 1079 95 L L M L T P M V A 0.016 1080 2 Y Y F L S M LS A 0.016 1081 192 I Y Y I P L I S L 0.016 1082 49 F T V M E S S V L0.015 1083 43 M F F I K F F T V 0.012 1084 23 M L S I F W F N V 0.0121085 59 A M A F D R F V A 0.012 1086 128 K L S C T D T R I 0.012 1087141 G L T A M F S T V 0.012 1088 154 L L I L L S Y V L 0.012 1089 186 HI V A F A I Y Y 0.012 1090 104 L L I R L S Y C H 0.012 1091 107 R L S YC H S Q V 0.012 1092 162 L I I R T V L S V 0.012 1093 216 T M I A N T YL L 0.012 1094 156 I L L S Y V L I I 0.012 1095 131 C T D T R I N S A0.010 1096 78 L T D S R I A Q I 0.010 1097 202 I V H R F G K Q A 0.0101098 38 A C L S H M F F I 0.009 1099 64 R F V A V S N P L 0.009 1100 84A Q I G V A S V I 0.009 1101 217 M I A N T Y L L I 0.008 1102 7 M L S AT D L G L 0.008 1103 240 Q I R R A V I K I 0.008 1104 194 Y I P L I S LS I 0.008 1105 228 L M N P V I Y S V 0.008 1106 121 C Y H P D V M K L0.008 1107 51 V M E S S V L L A 0.008 1108 168 L S V A S P E E R 0.0061109 127 M K L S C T D T R 0.006 1110 234 Y S V K T K Q I R 0.006 111124 L S I F W F N V R 0.006 1112 87 G V A S V I R G L 0.006 1113 19 T L VT M L S I F 0.006 1114 205 R F G K Q A P A Y 0.006 1115 221 T Y L L I SP L M 0.006 1116 70 N P L R Y A M I L 0.006 1117 155 L I L L S Y V L I0.006 1118 178 E T F S T C V S H 0.006 1119 75 A M I L T D S R I 0.0061120 66 V A V S N P L R Y 0.006 1121 102 V A L L I R L S Y 0.006 1122 96L M L T P M V A L 0.006 1123 153 L L L I L L S Y V 0.006 1124 165 R T VL S V A S P 0.005 1125 57 L L A M A F D R F 0.004 1126 28 W F N V R E IS F 0.004 1127 163 I I R T V L S V A 0.004 1128 139 A V G L T A M F S0.004 1129 143 T A M F S T V G V 0.004 1130 60 M A F D R F V A V 0.0041131 16 S I S T L V T M L 0.004 1132 110 Y C H S Q V L H H 0.004 1133 37N A C L S H M F F 0.004 1134 109 S Y C H S Q V L H 0.004 1135 119 S Y CY H P D V M 0.004 1136 189 A F A I Y Y I P L 0.004 1137 9 S A T D L G LS I 0.004 1138 224 L I S P L M N P V 0.004 1139 115 V L H H S Y C Y H0.004 1140 97 M L T P M V A L L 0.004 1141 152 D L L L I L L S Y 0.0041142 237 K T K Q I R R A V 0.003 1143 55 S V L L A M A F D 0.003 1144138 S A V G L T A M F 0.003 1145

TABLE XI V1B-A11-9mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 20 GV P G L E A F H 0.060 1146 9 I T S T S I I F L 0.020 1147 18 L T G V P GL E A 0.020 1148 52 A T I T Q P S L H 0.015 1149 42 A L L G N S L I L0.012 1150 23 G L E A F H T W I 0.012 1151 40 V T A L L G N S L 0.0101152 43 L L G N S L I L F 0.008 1153 8 N I T S T S I I F 0.008 1154 58 SL H E P M Y Y F 0.008 1155 32 S I P F C F L S V 0.008 1156 55 T Q P S LH E P M 0.006 1157 6 L Q N I T S T S I 0.006 1158 16 F L L T G V P G L0.006 1159 13 S I I F L L T G V 0.006 1160 1 F I T S T L Q N I 0.0041161 35 F C F L S V T A L 0.004 1162 30 W I S I P F C F L 0.004 1163 41T A L L G N S L I 0.003 1164 36 C F L S V T A L L 0.003 1165 25 E A F HT W I S I 0.002 1166 61 E P M Y Y F L S M 0.002 1167 51 F A T I T Q P SL 0.002 1168 39 S V T A L L G N S 0.002 1169 56 Q P S L H E P M Y 0.0021170 28 H T W I S I P F C 0.002 1171 11 S T S I I F L L T 0.002 1172 4 ST L Q N I T S T 0.002 1173 48 L I L F A T I T Q 0.001 1174 2 I T S T L QN I T 0.001 1175 54 I T Q P S L H E P 0.001 1176 29 T W I S I P F C F0.001 1177 37 F L S V T A L L G 0.001 1178 14 I I F L L T G V P 0.0011179 62 P M Y Y F L S M L 0.001 1180 49 I L F A T I T Q P 0.001 1181 53T I T Q P S L H E 0.001 1182 7 Q N I T S T S I I 0.001 1183 47 S L I L FA T I T 0.001 1184 10 T S T S I I F L L 0.001 1185 21 V P G L E A F H T0.001 1186 44 L G N S L I L F A 0.000 1187 59 L H E P M Y Y F L 0.0001188 5 T L Q N I T S T S 0.000 1189 27 F H T W I S I P F 0.000 1190 33 IP F C F L S V T 0.000 1191 17 L L T G V P G L E 0.000 1192 45 G N S L IL F A T 0.000 1193 19 T G V P G L E A F 0.000 1194 46 N S L I L F A T I0.000 1195 15 I F L L T G V P G 0.000 1196 34 P F C F L S V T A 0.0001197 26 A F H T W I S I P 0.000 1198 50 L F A T I T Q P S 0.000 1199 60H E P M Y Y F L S 0.000 1200 24 L E A F H T W I S 0.000 1201 31 I S I PF C F L S 0.000 1202 38 L S V T A L L G N 0.000 1203 57 P S L H E P M YY 0.000 1204 12 T S I I F L L T G 0.000 1205 3 T S T L Q N I T S 0.0001206 22 P G L E A F H T W 0.000 1207 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000

TABLE XI V2-A11-9mers SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 4 N T Y L L T SP L 0.020 1208 8 L T S P L M N P V 0.010 1209 5 T Y L L T S P L M 0.0061210 6 Y L L T S P L M N 0.001 1211 7 L L T S P L M N P 0.001 1212 1 M IA N T Y L L T 0.001 1213 2 I A N T Y L L T S 0.000 1214 9 T S P L M N PV I 0.000 1215 3 A N T Y L L T S P 0.000 1216

TABLE XII V1-A11-10-mers: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 Score SEQ ID55 S V L L A M A F D R 1.800 1217 199 S L S I V H R F G K 1.200 1218 38A C L S H M F F I K 0.900 1219 243 R A V I K I L H S K 0.900 1220 98 L TP M V A L L I R 0.400 1221 119 S Y C Y H P D V M K 0.400 1222 228 L M NP V I Y S V K 0.400 1223 73 R Y A M I L T D S R 0.240 1224 156 I L L S YV L I I R 0.240 1225 84 A Q I G V A S V I R 0.180 1226 64 R F V A V S NP L R 0.180 1227 230 N P V I Y S V K T K 0.150 1228 233 I Y S V K T K QI R 0.080 1229 50 T V M E S S V L L A 0.080 1230 23 M L S I F W F N V R0.080 1231 167 V L S V A S P E E R 0.080 1232 126 V M K L S C T D T R0.080 1233 20 L V T M L S I F W F 0.060 1234 87 G V A S V I R G L L0.060 1235 183 C V S H I V A F A I 0.060 1236 239 K Q I R R A V I K I0.054 1237 65 F V A V S N P L R Y 0.040 1238 101 M V A L L I R L S Y0.040 1239 67 A V S N P L R Y A M 0.040 1240 215 H T M I A N T Y L L0.040 1241 148 T V G V D L L L I L 0.040 1242 94 G L L M L T P M V A0.036 1243 168 L S V A S P E E R K 0.030 1244 147 S T V G V D L L L I0.030 1245 237 K T K Q I R R A V I 0.030 1246 114 Q V L H H S Y C Y H0.030 1247 42 H M F F I K F F T V 0.024 1248 135 R I N S A V G L T A0.024 1249 220 N T Y L L I S P L M 0.020 1250 213 Y V H T M I A N T Y0.020 1251 238 T K Q I R R A V I K 0.020 1252 113 S Q V L H H S Y C Y0.018 1253 22 T M L S I F W F N V 0.018 1254 208 K Q A P A Y V H T M0.018 1255 191 A I Y Y I P L I S L 0.016 1256 1 M Y Y F L S M L S A0.016 1257 18 S T L V T M L S I F 0.015 1258 49 F T V M E S S V L L0.015 1259 234 Y S V K T K Q I R R 0.012 1260 196 P L I S L S I V H R0.012 1261 58 L A M A F D R F V A 0.012 1262 150 G V D L L L I L L S0.012 1263 216 T M I A N T Y L L I 0.012 1264 193 Y Y I P L I S L S I0.012 1265 155 L I L L S Y V L I I 0.012 1266 107 R L S Y C H S Q V L0.012 1267 186 H I V A F A I Y Y I 0.012 1268 82 R I A Q I G V A S V0.012 1269 47 K F F T V M E S S V 0.012 1270 19 T L V T M L S I F W0.012 1271 153 L L L I L L S Y V L 0.012 1272 14 G L S I S T L V T M0.012 1273 6 S M L S A T D L G L 0.012 1274 161 V L I I R T V L S V0.012 1275 103 A L L I R L S Y C H 0.012 1276 131 C T D T R I N S A V0.010 1277 142 L T A M F S T V G V 0.010 1278 181 S T C V S H I V A F0.010 1279 109 S Y C H S Q V L H H 0.008 1280 144 A M F S T V G V D L0.008 1281 39 C L S H M F F I K F 0.008 1282 97 M L T P M V A L L I0.008 1283 120 Y C Y H P D V M K L 0.008 1284 51 V M E S S V L L A M0.008 1285 95 L L M L T P M V A L 0.008 1286 188 V A F A I Y Y I P L0.008 1287 99 T P M V A L L I R L 0.008 1288 223 L L I S P L M N P V0.006 1289 159 S Y V L I I R T V L 0.006 1290 154 L L I L L S Y V L I0.006 1291 162 L I I R T V L S V A 0.006 1292 37 N A C L S H M F F I0.006 1293 205 R F G K Q A P A Y V 0.006 1294 178 E T F S T C V S H I0.006 1295 139 A V G L T A M F S T 0.006 1296 90 S V I R G L L M L T0.006 1297 56 V L L A M A F D R F 0.006 1298 96 L M L T P M V A L L0.006 1299 195 I P L I S L S I V H 0.006 1300 165 R T V L S V A S P E0.005 1301 21 V T M L S I F W F N 0.004 1302 197 L I S L S I V H R F0.004 1303 232 V I Y S V K T K Q I 0.004 1304 74 Y A M I L T D S R I0.004 1305 43 M F F I K F F T V M 0.004 1306 187 I V A F A I Y Y I P0.004 1307 4 F L S M L S A T D L 0.004 1308 77 I L T D S R I A Q I 0.0041309 194 Y I P L I S L S I V 0.004 1310 224 L I S P L M N P V I 0.0041311 210 A P A Y V H T M I A 0.004 1312 88 V A S V I R G L L M 0.0041313 59 A M A F D R F V A V 0.004 1314 201 S I V H R F G K Q A 0.0031315 160 Y V L I I R T V L S 0.003 1316

TABLE XII V1B-A11-10mers Pos 1 2 3 4 5 6 7 8 9 0 Score SEQ ID 28 H T W IS I P F C F 0.060 1317 9 I T S T S I I F L L 0.030 1318 39 S V T A L L GN S L 0.020 1319 20 G V P G L E A F H T 0.018 1320 42 A L L G N S L I LF 0.012 1321 40 V T A L L G N S L I 0.010 1322 54 I T Q P S L H E P M0.010 1323 18 L T G V P G L E A F 0.010 1324 8 N I T S T S I I F L 0.0081325 58 S L H E P M Y Y F L 0.008 1326 17 L L T G V P G L E A 0.008 132743 L L G N S L I L F A 0.008 1328 55 T Q P S L H E P M Y 0.006 1329 6 LQ N I T S T S I I 0.006 1330 41 T A L L G N S L I L 0.006 1331 33 I P FC F L S V T A 0.004 1332 56 Q P S L H E P M Y Y 0.004 1333 26 A F H T WI S I P F 0.004 1334 5 T L Q N I T S T S I 0.004 1335 35 F C F L S V T AL L 0.004 1336 15 I F L L T G V P G L 0.003 1337 52 A T I T Q P S L H E0.003 1338 23 G L E A F H T W I S 0.002 1339 50 L F A T I T Q P S L0.002 1340 51 F A T I T Q P S L H 0.002 1341 11 S T S I I F L L T G0.002 1342 2 I T S T L Q N I T S 0.002 1343 21 V P G L E A F H T W 0.0021344 4 S T L Q N I T S T S 0.002 1345 47 S L I L F A T I T Q 0.001 13467 Q N I T S T S I I F 0.001 1347 30 W I S I P F C F L S 0.001 1348 45 GN S L I L F A T I 0.001 1349 24 L E A F H T W I S I 0.001 1350 60 H E PM Y Y F L S M 0.001 1351 61 E P M Y Y F L S M L 0.001 1352 49 I L F A TI T Q P S 0.001 1353 14 I I F L L T G V P G 0.001 1354 37 F L S V T A LL G N 0.001 1355 48 L I L F A T I T Q P 0.001 1356 36 C F L S V T A L LG 0.001 1357 16 F L L T G V P G L E 0.001 1358 31 I S I P F C F L S V0.001 1359 13 S I I F L L T G V P 0.001 1360 1 F I T S T L Q N I T 0.0001361 32 S I P F C F L S V T 0.000 1362 53 T I T Q P S L H E P 0.000 136329 T W I S I P F C F L 0.000 1364 19 T G V P G L E A F H 0.000 1365 12 TS I I F L L T G V 0.000 1366 34 P F C F L S V T A L 0.000 1367 62 P M YY F L S M L S 0.000 1368 25 E A F H T W I S I P 0.000 1369 57 P S L H EP M Y Y F 0.000 1370 44 L G N S L I L F A T 0.000 1371 59 L H E P M Y YF L S 0.000 1372 10 T S T S I I F L L T 0.000 1373 22 P G L E A F H T WI 0.000 1374 38 L S V T A L L G N S 0.000 1375 46 N S L I L F A T I T0.000 1376 27 F H T W I S I P F C 0.000 1377 3 T S T L Q N I T S T 0.0001378 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000

TABLE XII V2-A11-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 5N T Y L L T S P L M 0.020 1379 9 L T S P L M N P V I 0.010 1380 8 L L TS P L M N P V 0.004 1381 7 Y L L T S P L M N P 0.001 1382 6 T Y L L T SP L M N 0.001 1383 1 T M I A N T Y L L T 0.001 1384 2 M I A N T Y L L TS 0.001 1385 4 A N T Y L L T S P L 0.000 1386 3 I A N T Y L L T S P0.000 1387 10 T S P L M N P V I Y 0.000 1388

TABLE XIII V1-A24-9-mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 121C Y H P D V M K L 264.000 1389 192 I Y Y I P L I S L 200.000 1390 64 R FV A V S N P L 100.800 1391 221 T Y L L I S P L M 52.500 1392 233 I Y S VK T K Q I 50.000 1393 145 M F S T V G V D L 28.000 1394 119 S Y C Y H PD V M 25.000 1395 189 A F A I Y Y I P L 20.000 1396 28 W F N V R E I S F15.000 1397 73 R Y A M I L T D S 14.000 1398 193 Y Y I P L I S L S10.800 1399 159 S Y V L I I R T V 10.500 1400 149 V G V D L L L I L8.640 1401 147 S T V G V D L L L 8.400 1402 160 Y V L I I R T V L 8.4001403 212 A Y V H T M I A N 7.500 1404 154 L L I L L S Y V L 7.200 140550 T V M E S S V L L 7.200 1406 96 L M L T P M V A L 6.000 1407 5 L S ML S A T D L 6.000 1408 216 T M I A N T Y L L 6.000 1409 49 F T V M E S SV L 6.000 1410 70 N P L R Y A M I L 6.000 1411 1 M Y Y F L S M L S 6.0001412 215 H T M I A N T Y L 6.000 1413 90 S V I R G L L M L 6.000 1414 88V A S V I R G L L 5.600 1415 87 G V A S V I R G L 5.600 1416 26 I F W FN V R E I 5.500 1417 179 T F S T C V S H I 5.000 1418 2 Y Y F L S M L SA 5.000 1419 16 S I S T L V T M L 4.800 1420 108 L S Y C H S Q V L 4.8001421 97 M L T P M V A L L 4.800 1422 150 G V D L L L I L L 4.800 1423220 N T Y L L I S P L 4.800 1424 44 F F I K F F T V M 4.500 1425 198 I SL S I V H R F 4.200 1426 146 F S T V G V D L L 4.000 1427 7 M L S A T DL G L 4.000 1428 12 D L G L S I S T L 4.000 1429 35 S F N A C L S H M3.750 1430 138 S A V G L T A M F 3.600 1431 172 S P E E R K E T F 3.6001432 54 S S V L L A M A F 3.600 1433 21 V T M L S I F W F 3.000 1434 182T C V S H I V A F 3.000 1435 19 T L V T M L S I F 3.000 1436 40 L S H MF F I K F 2.640 1437 57 L L A M A F D R F 2.400 1438 36 F N A C L S H MF 2.400 1439 98 L T P M V A L L I 2.100 1440 194 Y I P L I S L S I 2.1001441 84 A Q I G V A S V I 2.100 1442 128 K L S C T D T R I 2.000 1443 37N A C L S H M F F 2.000 1444 190 F A I Y Y I P L I 1.500 1445 156 I L LS Y V L I I 1.500 1446 69 S N P L R Y A M I 1.500 1447 75 A M I L T D SR I 1.500 1448 225 I S P L M N P V I 1.500 1449 18 S T L V T M L S I1.500 1450 155 L I L L S Y V L I 1.500 1451 93 R G L L M L T P M 1.5001452 38 A C L S H M F F I 1.500 1453 9 S A T D L G L S I 1.440 1454 47 KF F T V M E S S 1.400 1455 210 A P A Y V H T M I 1.400 1456 184 V S H IV A F A I 1.400 1457 32 R E I S F N A C L 1.200 1458 240 Q I R R A V I KI 1.100 1459 68 V S N P L R Y A M 1.080 1460 205 R F G K Q A P A Y 1.0001461 217 M I A N T Y L L I 1.000 1462 187 I V A F A I Y Y I 1.000 1463148 T V G V D L L L I 1.000 1464 78 L T D S R I A Q I 1.000 1465 89 A SV I R G L L M 0.750 1466 3 Y F L S M L S A T 0.750 1467 209 Q A P A Y VH T M 0.750 1468 15 L S I S T L V T M 0.750 1469 100 P M V A L L I R L0.720 1470 134 T R I N S A V G L 0.600 1471 43 M F F I K F F T V 0.6001472 241 I R R A V I K I L 0.560 1473 48 F F T V M E S S V 0.500 1474137 N S A V G L T A M 0.500 1475 61 A F D R F V A V S 0.500 1476 109 S YC H S Q V L H 0.500 1477 243 R A V I K I L H S 0.300 1478 41 S H M F F IK F F 0.300 1479 135 R I N S A V G L T 0.300 1480 237 K T K Q I R R A V0.280 1481 82 R I A Q I G V A S 0.280 1482 22 T M L S I F W F N 0.2521483 228 L M N P V I Y S V 0.252 1484 208 K Q A P A Y V H T 0.240 1485152 D L L L I L L S Y 0.210 1486 13 L G L S I S T L V 0.210 1487 102 V AL L I R L S Y 0.210 1488

TABLE XIII V1B-A24-9mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 36C F L S V T A L L 42.000 1489 42 A L L G N S L I L 6.000 1490 16 F L L TG V P G L 6.000 1491 40 V T A L L G N S L 5.760 1492 10 T S T S I I F LL 5.600 1493 30 W I S I P F C F L 4.800 1494 29 T W I S I P F C F 4.2001495 51 F A T I T Q P S L 4.000 1496 9 I T S T S I I F L 4.000 1497 35 FC F L S V T A L 4.000 1498 19 T G V P G L E A F 3.600 1499 58 S L H E PM Y Y F 2.400 1500 46 N S L I L F A T I 2.160 1501 43 L L G N S L I L F2.000 1502 8 N I T S T S I I F 2.000 1503 7 Q N I T S T S I I 1.500 150441 T A L L G N S L I 1.500 1505 6 L Q N I T S T S I 1.500 1506 23 G L EA F H T W I 1.500 1507 1 F I T S T L Q N I 1.200 1508 25 E A F H T W I SI 1.000 1509 61 E P M Y Y F L S M 0.900 1510 55 T Q P S L H E P M 0.9001511 50 L F A T I T Q P S 0.840 1512 59 L H E P M Y Y F L 0.720 1513 62P M Y Y F L S M L 0.400 1514 27 F H T W I S I P F 0.280 1515 5 T L Q N IT S T S 0.210 1516 31 I S I P F C F L S 0.180 1517 44 L G N S L I L F A0.180 1518 13 S I I F L L T G V 0.180 1519 32 S I P F C F L S V 0.1801520 11 S T S I I F L L T 0.168 1521 47 S L I L F A T I T 0.150 1522 4 ST L Q N I T S T 0.150 1523 38 L S V T A L L G N 0.150 1524 2 I T S T L QN I T 0.144 1525 45 G N S L I L F A T 0.140 1526 39 S V T A L L G N S0.120 1527 18 L T G V P G L E A 0.110 1528 56 Q P S L H E P M Y 0.1001529 28 H T W I S I P F C 0.100 1530 3 T S T L Q N I T S 0.100 1531 33 IP F C F L S V T 0.100 1532 21 V P G L E A F H T 0.100 1533 15 I F L L TG V P G 0.075 1534 34 P F C F L S V T A 0.060 1535 26 A F H T W I S I P0.050 1536 22 P G L E A F H T W 0.022 1537 54 I T Q P S L H E P 0.0201538 20 G V P G L E A F H 0.018 1539 12 T S I I F L L T G 0.015 1540 48L I L F A T I T Q 0.015 1541 57 P S L H E P M Y Y 0.015 1542 52 A T I TQ P S L H 0.015 1543 60 H E P M Y Y F L S 0.015 1544 17 L L T G V P G LE 0.014 1545 14 I I F L L T G V P 0.012 1546 24 L E A F H T W I S 0.0101547 49 I L F A T I T Q P 0.010 1548 37 F L S V T A L L G 0.010 1549 53T I T Q P S L H E 0.010 1550 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000

TABLE XIII V2-A24-9mers SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 5 T Y L L T SP L M 37.500 1551 4 N T Y L L T S P L 4.800 1552 9 T S P L M N P V I1.500 1553 8 L T S P L M N P V 0.173 1554 6 Y L L T S P L M N 0.150 15552 I A N T Y L L T S 0.150 1556 1 M I A N T Y L L T 0.100 1557 3 A N T YL L T S P 0.012 1558 7 L L T S P L M N P 0.010 1559

TABLE XIV V1-A24-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID159 S Y V L I I R 15 T V L 420.000 1560 193 Y Y I P L I S L S I 126.0001561 145 M F S T V G V D L L 20.000 1562 48 F F T V M E S S V L 20.0001563 35 S F N A C L S H M F 18.000 1564 107 R L S Y C H S Q V L 9.6001565 149 V G V D L L L I L L 8.640 1566 121 C Y H P D V M K L S 8.4001567 86 I G V A S V I R G L 8.400 1568 221 T Y L L I S P L M N 7.5001569 212 A Y V H T M I A N T 7.500 1570 99 T P M V A L L I R L 7.2001571 15 L S I S T L V T M L 7.200 1572 153 L L L I L L S Y V L 7.2001573 6 S M L S A T D L G L 6.000 1574 49 F T V M E S S V L L 6.000 157569 S N P L R Y A M I L 6.000 1576 96 L M L T P M V A L L 6.000 1577 89 AS V I R G L L M L 6.000 1578 95 L L M L T P M V A L 6.000 1579 192 I Y YI P L I S L S 6.000 1580 215 H T M I A N T Y L L 6.000 1581 144 A M F ST V G V D L 5.600 1582 146 F S T V G V D L L L 5.600 1583 240 Q I R R AV I K I L 5.600 1584 87 G V A S V I R G L L 5.600 1585 2 Y Y F L S M L SA T 5.000 1586 1 M Y Y F L S M L S A 5.000 1587 189 A F A I Y Y I P L I5.000 1588 219 A N T Y L L I S P L 4.800 1589 148 T V G V D L L L I L4.800 1590 120 Y C Y H P D V M K L 4.400 1591 133 D T R I N S A V G L4.000 1592 188 V A F A I Y Y I P L 4.000 1593 4 F L S M L S A T D L4.000 1594 191 A I Y Y I P L I S L 4.000 1595 56 V L L A M A F D R F3.600 1596 171 A S P E E R K E T F 3.600 1597 239 K Q I R R A V I K I3.300 1598 43 M F F I K F F T V M 3.000 1599 18 S T L V T M L S I F3.000 1600 197 L I S L S I V H R F 2.800 1601 39 C L S H M F F I K F2.640 1602 53 E S S V L L A M A F 2.400 1603 137 N S A V G L T A M F2.400 1604 209 Q A P A Y V H T M I 2.100 1605 83 I A Q I G V A S V I2.100 1606 237 K T K Q I R R A V I 2.000 1607 36 F N A C L S H M F F2.000 1608 181 S T C V S H I V A F 2.000 1609 27 F W F N V R E I S F2.000 1610 40 L S H M F F I K F F 2.000 1611 20 L V T M L S I F W F2.000 1612 68 V S N P L R Y A M I 1.800 1613 97 M L T P M V A L L I1.680 1614 74 Y A M I L T D S R I 1.500 1615 154 L L I L L S Y V L I1.500 1616 155 L I L L S Y V L I I 1.500 1617 186 H I V A F A I Y Y I1.500 1618 147 S T V G V D L L L I 1.500 1619 216 T M I A N T Y L L I1.500 1620 183 C V S H I V A F A I 1.400 1621 224 L I S P L M N P V I1.200 1622 77 I L T D S R I A Q I 1.200 1623 8 L S A T D L G L S I 1.2001624 208 K Q A P A Y V H T M 1.200 1625 73 R Y A M I L T D S R 1.2001626 25 S I F W F N V R E I 1.100 1627 51 V M E S S V L L A M 1.050 1628232 V I Y S V K T K Q I 1.000 1629 178 E T F S T C V S H I 1.000 1630 37N A C L S H M F F I 1.000 1631 17 I S T L V T M L S I 1.000 1632 205 R FG K Q A P A Y V 1.000 1633 47 K F F T V M E S S V 1.000 1634 28 W F N VR E I S F N 0.750 1635 26 I F W F N V R E I S 0.700 1636 220 N T Y L L IS P L M 0.700 1637 61 A F D R F V A V S N 0.700 1638 179 T F S T C V S HI V 0.700 1639 63 D R F V A V S N P L 0.672 1640 11 T D L G L S I S T L0.600 1641 67 A V S N P L R Y A M 0.600 1642 233 I Y S V K T K Q I R0.600 1643 31 V R E I S F N A C L 0.600 1644 14 G L S I S T L V T M0.500 1645 88 V A S V I R G L L M 0.500 1646 118 H S Y C Y H P D V M0.500 1647 119 S Y C Y H P D V M K 0.500 1648 34 I S F N A C L S H M0.500 1649 109 S Y C H S Q V L H H 0.500 1650 136 I N S A V G L T A M0.500 1651 135 R I N S A V G L T A 0.420 1652 214 V H T M I A N T Y L0.400 1653 93 R G L L M L T P M V 0.360 1654 21 V T M L S I F W F N0.252 1655 223 L L I S P L M N P V 0.216 1656 190 F A I Y Y I P L I S0.210 1657 162 L I I R T V L S V A 0.210 1658 29 F N V R E I S F N A0.210 1659

TABLE XIV V1B-A24-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID15 I F L L T G V P G L 30.000 1660 50 L F A T I T Q P S L 20.000 1661 26A F H T W I S I P F 14.000 1662 29 T W I S I P F C F L 7.200 1663 41 T AL L G N S L I L 6.000 1664 61 E P M Y Y F L S M L 6.000 1665 39 S V T AL L G N S L 5.760 1666 35 F C F L S V T A L L 5.600 1667 9 I T S T S I IF L L 5.600 1668 58 S L H E P M Y Y F L 4.800 1669 8 N I T S T S I I F L4.000 1670 7 Q N I T S T S I I F 3.000 1671 42 A L L G N S L I L F 3.0001672 28 H T W I S I P F C F 2.800 1673 34 P F C F L S V T A L 2.000 167418 L T G V P G L E A F 2.000 1675 5 T L Q N I T S T S I 1.500 1676 6 L QN I T S T S I I 1.500 1677 45 G N S L I L F A T I 1.440 1678 54 I T Q PS L H E P M 1.080 1679 40 V T A L L G N S L I 1.000 1680 57 P S L H E PM Y Y F 0.300 1681 31 I S I P F C F L S V 0.216 1682 4 S T L Q N I T S TS 0.210 1683 44 L G N S L I L F A T 0.210 1684 22 P G L E A F H T W I0.180 1685 12 T S I I F L L T G V 0.180 1686 38 L S V T A L L G N S0.180 1687 10 T S T S I I F L L T 0.168 1688 49 I L F A T I T Q P S0.168 1689 20 G V P G L E A F H T 0.150 1690 32 S I P F C F L S V T0.150 1691 46 N S L I L F A T I T 0.150 1692 23 G L E A F H T W I S0.150 1693 55 T Q P S L H E P M Y 0.150 1694 1 F I T S T L Q N I T 0.1441695 43 L L G N S L I L F A 0.120 1696 33 I P F C F L S V T A 0.120 169721 V P G L E A F H T W 0.120 1698 17 L L T G V P G L E A 0.110 1699 3 TS T L Q N I T S T 0.100 1700 56 Q P S L H E P M Y Y 0.100 1701 24 L E AF H T W I S I 0.100 1702 30 W I S I P F C F L S 0.100 1703 37 F L S V TA L L G N 0.100 1704 2 I T S T L Q N I T S 0.100 1705 60 H E P M Y Y F LS M 0.090 1706 36 C F L S V T A L L G 0.075 1707 19 T G V P G L E A F H0.022 1708 16 F L L T G V P G L E 0.021 1709 59 L H E P M Y Y F L S0.018 1710 13 S I I F L L T G V P 0.018 1711 48 L I L F A T I T Q P0.015 1712 52 A T I T Q P S L H E 0.015 1713 47 S L I L F A T I T Q0.015 1714 62 P M Y Y F L S M L S 0.012 1715 53 T I T Q P S L H E P0.011 1716 14 I I F L L T G V P G 0.010 1717 27 F H T W I S I P F C0.010 1718 11 S T S I I F L L T G 0.010 1719 25 E A F H T W I S I P0.010 1720 51 F A T I T Q P S L H 0.010 1721 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000

TABLE XIV V2-A24-10mers SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 6 T Y L L TS P L M N 7.500 1722 4 A N T Y L L T S P L 4.800 1723 9 L T S P L M N PV I 1.200 1724 5 N T Y L L T S P L M 0.500 1725 1 T M I A N T Y L L T0.150 1726 10 T S P L M N P V I Y 0.150 1727 8 L L T S P L M N P V 0.1441728 2 M I A N T Y L L T S 0.100 1729 3 I A N T Y L L T S P 0.018 1730 7Y L L T S P L M N P 0.015 1731

TABLE XV V1-B7-9-mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 70 N PL R Y A M I L 80.000 1732 50 T V M E S S V L L 60.000 1733 160 Y V L I IR T V L 30.000 1734 210 A P A Y V H T M I 24.000 1735 90 S V I R G L L ML 20.000 1736 87 G V A S V I R G L 20.000 1737 88 V A S V I R G L L18.000 1738 215 H T M I A N T Y L 12.000 1739 5 L S M L S A T D L 12.0001740 150 G V D L L L I L L 6.000 1741 96 L M L T P M V A L 6.000 1742 30N V R E I S F N A 5.000 1743 108 L S Y C H S Q V L 4.000 1744 16 S I S TL V T M L 4.000 1745 154 L L I L L S Y V L 4.000 1746 241 I R R A V I KI L 4.000 1747 146 F S T V G V D L L 4.000 1748 149 V G V D L L L I L4.000 1749 240 Q I R R A V I K I 4.000 1750 216 T M I A N T Y L L 4.0001751 220 N T Y L L I S P L 4.000 1752 49 F T V M E S S V L 4.000 1753195 I P L I S L S I V 4.000 1754 7 M L S A T D L G L 4.000 1755 147 S TV G V D L L L 4.000 1756 12 D L G L S I S T L 4.000 1757 97 M L T P M VA L L 4.000 1758 89 A S V I R G L L M 3.000 1759 209 Q A P A Y V H T M3.000 1760 67 A V S N P L R Y A 2.250 1761 148 T V G V D L L L I 2.0001762 80 D S R I A Q I G V 2.000 1763 230 N P V I Y S V K T 2.000 1764187 I V A F A I Y Y I 2.000 1765 58 L A M A F D R F V 1.800 1766 143 T AM F S T V G V 1.800 1767 68 V S N P L R Y A M 1.500 1768 189 A F A I Y YI P L 1.200 1769 9 S A T D L G L S I 1.200 1770 75 A M I L T D S R I1.200 1771 190 F A I Y Y I P L I 1.200 1772 38 A C L S H M F F I 1.2001773 84 A Q I G V A S V I 1.200 1774 93 R G L L M L T P M 1.000 1775 163I I R T V L S V A 1.000 1776 91 V I R G L L M L T 1.000 1777 15 L S I ST L V T M 1.000 1778 137 N S A V G L T A M 1.000 1779 60 M A F D R F V AV 0.600 1780 123 H P D V M K L S C 0.600 1781 99 T P M V A L L I R 0.6001782 83 I A Q I G V A S V 0.600 1783 192 I Y Y I P L I S L 0.600 1784213 Y V H T M I A N T 0.500 1785 202 I V H R F G K Q A 0.500 1786 183 CV S H I V A F A 0.500 1787 171 A S P E E R K E T 0.450 1788 59 A M A F DR F V A 0.450 1789 64 R F V A V S N P L 0.400 1790 69 S N P L R Y A M I0.400 1791 98 L T P M V A L L I 0.400 1792 121 C Y H P D V M K L 0.4001793 32 R E I S F N A C L 0.400 1794 18 S T L V T M L S I 0.400 1795 217M I A N T Y L L I 0.400 1796 145 M F S T V G V D L 0.400 1797 100 P M VA L L I R L 0.400 1798 128 K L S C T D T R I 0.400 1799 184 V S H I V AF A I 0.400 1800 194 Y I P L I S L S I 0.400 1801 155 L I L L S Y V L I0.400 1802 134 T R I N S A V G L 0.400 1803 225 I S P L M N P V I 0.4001804 156 I L L S Y V L I I 0.400 1805 226 S P L M N P V I Y 0.400 1806237 K T K Q I R R A V 0.300 1807 103 A L L I R L S Y C 0.300 1808 139 AV G L T A M F S 0.300 1809 95 L L M L T P M V A 0.300 1810 13 L G L S IS T L V 0.200 1811 105 L I R L S Y C H S 0.200 1812 23 M L S I F W F N V0.200 1813 162 L I I R T V L S V 0.200 1814 153 L L L I L L S Y V 0.2001815 206 F G K Q A P A Y V 0.200 1816 94 G L L M L T P M V 0.200 1817180 F S T C V S H I V 0.200 1818 107 R L S Y C H S Q V 0.200 1819 228 LM N P V I Y S V 0.200 1820 141 G L T A M F S T V 0.200 1821 224 L I S PL M N P V 0.200 1822 118 H S Y C Y H P D V 0.200 1823 125 D V M K L S CT D 0.150 1824 244 A V I K I L H S K 0.150 1825 172 S P E E R K E T F0.120 1826 78 L T D S R I A Q I 0.120 1827 52 M E S S V L L A M 0.1001828 14 G L S I S T L V T 0.100 1829 158 L S Y V L I I R T 0.100 1830119 S Y C Y H P D V M 0.100 1831

TABLE XV V1B-B7-9mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 61 E PM Y Y F L S M 60.000 1832 51 F A T I T Q P S L 12.000 1833 42 A L L G NS L I L 12.000 1834 30 W I S I P F C F L 6.000 1835 16 F L L T G V P G L4.000 1836 10 T S T S I I F L L 4.000 1837 40 V T A L L G N S L 4.0001838 35 F C F L S V T A L 4.000 1839 9 I T S T S I I F L 4.000 1840 21 VP G L E A F H T 2.000 1841 33 I P F C F L S V T 2.000 1842 25 E A F H TW I S I 1.200 1843 41 T A L L G N S L I 1.200 1844 55 T Q P S L H E P M1.000 1845 36 C F L S V T A L L 0.400 1846 7 Q N I T S T S I I 0.4001847 1 F I T S T L Q N I 0.400 1848 46 N S L I L F A T I 0.400 1849 56 QP S L H E P M Y 0.400 1850 6 L Q N I T S T S I 0.400 1851 62 P M Y Y F LS M L 0.400 1852 13 S I I F L L T G V 0.200 1853 32 S I P F C F L S V0.200 1854 18 L T G V P G L E A 0.150 1855 59 L H E P M Y Y F L 0.1201856 23 G L E A F H T W I 0.120 1857 45 G N S L I L F A T 0.100 1858 47S L I L F A T I T 0.100 1859 44 L G N S L I L F A 0.100 1860 4 S T L Q NI T S T 0.100 1861 11 S T S I I F L L T 0.100 1862 2 I T S T L Q N I T0.100 1863 39 S V T A L L G N S 0.100 1864 28 H T W I S I P F C 0.1001865 20 G V P G L E A F H 0.050 1866 58 S L H E P M Y Y F 0.030 1867 52A T I T Q P S L H 0.030 1868 38 L S V T A L L G N 0.020 1869 5 T L Q N IT S T S 0.020 1870 43 L L G N S L I L F 0.020 1871 31 I S I P F C F L S0.020 1872 19 T G V P G L E A F 0.020 1873 3 T S T L Q N I T S 0.0201874 8 N I T S T S I I F 0.020 1875 53 T I T Q P S L H E 0.015 1876 54 IT Q P S L H E P 0.010 1877 14 I I F L L T G V P 0.010 1878 37 F L S V TA L L G 0.010 1879 49 I L F A T I T Q P 0.010 1880 48 L I L F A T I T Q0.010 1881 12 T S I I F L L T G 0.010 1882 17 L L T G V P G L E 0.0101883 26 A F H T W I S I P 0.003 1884 29 T W I S I P F C F 0.002 1885 50L F A T I T Q P S 0.002 1886 27 F H T W I S I P F 0.002 1887 22 P G L EA F H T W 0.002 1888 24 L E A F H T W I S 0.002 1889 60 H E P M Y Y F LS 0.002 1890 57 P S L H E P M Y Y 0.002 1891 15 I F L L T G V P G 0.0011892 34 P F C F L S V T A 0.001 1893 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000

TABLE XV V2-B7-9mers-238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 4 N T YL L T S P L 4.000 1894 9 T S P L M N P V I 0.400 1895 8 L T S P L M N PV 0.200 1896 5 T Y L L T S P L M 0.100 1897 1 M I A N T Y L L T 0.1001898 2 I A N T Y L L T S 0.060 1899 3 A N T Y L L T S P 0.030 1900 6 Y LL T S P L M N 0.020 1901 7 L L T S P L M N P 0.015 1902

TABLE XVI V1-B7-10-mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 99T P M V A L L I R L 240.000 1903 133 D T R I N S A V G L 40.000 1904 240Q I R R A V I K I L 40.000 1905 87 G V A S V I R G L L 30.000 1906 67 AV S N P L R Y A M 22.500 1907 148 T V G V D L L L I L 20.000 1908 191 AI Y Y I P L I S L 18.000 1909 95 L L M L T P M V A L 18.000 1910 219 A NT Y L L I S P L 12.000 1911 144 A M F S T V G V D L 12.000 1912 89 A S VI R G L L M L 12.000 1913 215 H T M I A N T Y L L 12.000 1914 188 V A FA I Y Y I P L 12.000 1915 210 A P A Y V H T M I A 6.000 1916 30 N V R EI S F N A C 5.000 1917 86 I G V A S V I R G L 4.000 1918 107 R L S Y C HS Q V L 4.000 1919 149 V G V D L L L I L L 4.000 1920 146 F S T V G V DL L L 4.000 1921 69 S N P L R Y A M I L 4.000 1922 96 L M L T P M V A LL 4.000 1923 49 F T V M E S S V L L 4.000 1924 6 S M L S A T D L G L4.000 1925 4 F L S M L S A T D L 4.000 1926 120 Y C Y H P D V M K L4.000 1927 15 L S I S T L V T M L 4.000 1928 153 L L L I L L S Y V L4.000 1929 74 Y A M I L T D S R I 3.600 1930 88 V A S V I R G L L M3.000 1931 183 C V S H I V A F A I 2.000 1932 70 N P L R Y A M I L T2.000 1933 139 A V G L T A M F S T 1.500 1934 125 D V M K L S C T D T1.500 1935 50 T V M E S S V L L A 1.500 1936 58 L A M A F D R F V A1.350 1937 209 Q A P A Y V H T M I 1.200 1938 37 N A C L S H M F F I1.200 1939 83 I A Q I G V A S V I 1.200 1940 80 D S R I A Q I G V A1.000 1941 220 N T Y L L I S P L M 1.000 1942 34 I S F N A C L S H M1.000 1943 118 H S Y C Y H P D V M 1.000 1944 136 I N S A V G L T A M1.000 1945 208 K Q A P A Y V H T M 1.000 1946 14 G L S I S T L V T M1.000 1947 59 A M A F D R F V A V 0.600 1948 237 K T K Q I R R A V I0.600 1949 226 S P L M N P V I Y S 0.600 1950 123 H P D V M K L S C T0.600 1951 159 S Y V L I I R T V L 0.600 1952 90 S V I R G L L M L T0.500 1953 235 S V K T K Q I R R A 0.500 1954 66 V A V S N P L R Y A0.450 1955 170 V A S P E E R K E T 0.450 1956 224 L I S P L M N P V I0.400 1957 48 F F T V M E S S V L 0.400 1958 214 V H T M I A N T Y L0.400 1959 154 L L I L L S Y V L I 0.400 1960 25 S I F W F N V R E I0.400 1961 8 L S A T D L G L S I 0.400 1962 232 V I Y S V K T K Q I0.400 1963 11 T D L G L S I S T L 0.400 1964 97 M L T P M V A L L I0.400 1965 17 I S T L V T M L S I 0.400 1966 186 H I V A F A I Y Y I0.400 1967 239 K Q I R R A V I K I 0.400 1968 216 T M I A N T Y L L I0.400 1969 145 M F S T V G V D L L 0.400 1970 68 V S N P L R Y A M I0.400 1971 77 I L T D S R I A Q I 0.400 1972 147 S T V G V D L L L I0.400 1973 63 D R F V A V S N P L 0.400 1974 155 L I L L S Y V L I I0.400 1975 178 E T F S T C V S H I 0.400 1976 75 A M I L T D S R I A0.300 1977 51 V M E S S V L L A M 0.300 1978 102 V A L L I R L S Y C0.300 1979 223 L L I S P L M N P V 0.200 1980 195 I P L I S L S I V H0.200 1981 161 V L I I R T V L S V 0.200 1982 142 L T A M F S T V G V0.200 1983 194 Y I P L I S L S I V 0.200 1984 230 N P V I Y S V K T K0.200 1985 93 R G L L M L T P M V 0.200 1986 57 L L A M A F D R F V0.200 1987 152 D L L L I L L S Y V 0.200 1988 140 V G L T A M F S T V0.200 1989 158 L S Y V L I I R T V 0.200 1990 42 H M F F I K F F T V0.200 1991 82 R I A Q I G V A S V 0.200 1992 163 I I R T V L S V A S0.200 1993 22 T M L S I F W F N V 0.200 1994 12 D L G L S I S T L V0.200 1995 101 M V A L L I R L S Y 0.150 1996 244 A V I K I L H S K E0.150 1997 172 S P E E R K E T F S 0.120 1998 189 A F A I Y Y I P L I0.120 1999 31 V R E I S F N A C L 0.120 2000 92 I R G L L M L T P M0.100 2001 160 Y V L I I R T V L S 0.100 2002

TABLE XVI V1B-B7-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 61E P M Y Y F L S M L 240.000 2003 39 S V T A L L G N S L 20.000 2004 41 TA L L G N S L I L 12.000 2005 35 F C F L S V T A L L 4.000 2006 58 S L HE P M Y Y F L 4.000 2007 9 I T S T S I I F L L 4.000 2008 8 N I T S T SI I F L 4.000 2009 33 I P F C F L S V T A 2.000 2010 54 I T Q P S L H EP M 1.000 2011 29 T W I S I P F C F L 0.600 2012 20 G V P G L E A F H T0.500 2013 50 L F A T I T Q P S L 0.400 2014 56 Q P S L H E P M Y Y0.400 2015 40 V T A L L G N S L I 0.400 2016 6 L Q N I T S T S I I 0.4002017 45 G N S L I L F A T I 0.400 2018 15 I F L L T G V P G L 0.400 20195 T L Q N I T S T S I 0.400 2020 21 V P G L E A F H T W 0.400 2021 31 IS I P F C F L S V 0.200 2022 12 T S I I F L L T G V 0.200 2023 17 L L TG V P G L E A 0.150 2024 44 L G N S L I L F A T 0.100 2025 32 S I P F CF L S V T 0.100 2026 10 T S T S I I F L L T 0.100 2027 3 T S T L Q N I TS T 0.100 2028 43 L L G N S L I L F A 0.100 2029 60 H E P M Y Y F L S M0.100 2030 46 N S L I L F A T I T 0.100 2031 1 F I T S T L Q N I T 0.1002032 42 A L L G N S L I L F 0.060 2033 52 A T I T Q P S L H E 0.045 203434 P F C F L S V T A L 0.040 2035 22 P G L E A F H T W I 0.040 2036 24 LE A F H T W I S I 0.040 2037 51 F A T I T Q P S L H 0.030 2038 25 E A FH T W I S I P 0.030 2039 18 L T G V P G L E A F 0.020 2040 30 W I S I PF C F L S 0.020 2041 37 F L S V T A L L G N 0.020 2042 38 L S V T A L LG N S 0.020 2043 49 I L F A T I T Q P S 0.020 2044 4 S T L Q N I T S T S0.020 2045 28 H T W I S I P F C F 0.020 2046 7 Q N I T S T S I I F 0.0202047 2 I T S T L Q N I T S 0.020 2048 55 T Q P S L H E P M Y 0.020 204919 T G V P G L E A F H 0.010 2050 48 L I L F A T I T Q P 0.010 2051 53 TI T Q P S L H E P 0.010 2052 14 I I F L L T G V P G 0.010 2053 13 S I IF L L T G V P 0.010 2054 47 S L I L F A T I T Q 0.010 2055 11 S T S I IF L L T G 0.010 2056 16 F L L T G V P G L E 0.010 2057 27 F H T W I S IP F C 0.010 2058 26 A F H T W I S I P F 0.006 2059 23 G L E A F H T W IS 0.006 2060 57 P S L H E P M Y Y F 0.003 2061 62 P M Y Y F L S M L S0.002 2062 36 C F L S V T A L L G 0.001 2063 59 L H E P M Y Y F L S0.001 2064 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000

TABLE XVI V2-B7-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID 4 AN T Y L L T S P L 12.000 2065 5 N T Y L L T S P L M 1.000 2066 9 L T S PL M N P V I 0.400 2067 8 L L T S P L M N P V 0.200 2068 1 T M I A N T YL L T 0.100 2069 3 I A N T Y L L T S P 0.030 2070 10 T S P L M N P V I Y0.020 2071 2 M I A N T Y L L T S 0.020 2072 7 Y L L T S P L M N P 0.0152073 6 T Y L L T S P L M N 0.002 2074

TABLE XVII V1-B35-9-mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 226S P L M N P V I Y 40.000 2075 70 N P L R Y A M I L 20.000 2076 172 S P EE R K E T F 12.000 2077 68 V S N P L R Y A M 10.000 2078 89 A S V I R GL L M 10.000 2079 137 N S A V G L T A M 10.000 2080 112 H S Q V L H H SY 10.000 2081 15 L S I S T L V T M 10.000 2082 210 A P A Y V H T M I8.000 2083 209 Q A P A Y V H T M 6.000 2084 102 V A L L I R L S Y 6.0002085 66 V A V S N P L R Y 6.000 2086 146 F S T V G V D L L 5.000 2087 5L S M L S A T D L 5.000 2088 54 S S V L L A M A F 5.000 2089 40 L S H MF F I K F 5.000 2090 108 L S Y C H S Q V L 5.000 2091 198 I S L S I V HR F 5.000 2092 195 I P L I S L S I V 4.000 2093 93 R G L L M L T P M4.000 2094 80 D S R I A Q I G V 3.000 2095 88 V A S V I R G L L 3.0002096 37 N A C L S H M F F 3.000 2097 138 S A V G L T A M F 3.000 2098 9S A T D L G L S I 2.400 2099 186 H I V A F A I Y Y 2.000 2100 225 I S PL M N P V I 2.000 2101 50 T V M E S S V L L 2.000 2102 230 N P V I Y S VK T 2.000 2103 152 D L L L I L L S Y 2.000 2104 114 Q V L H H S Y C Y2.000 2105 149 V G V D L L L I L 2.000 2106 184 V S H I V A F A I 2.0002107 49 F T V M E S S V L 1.500 2108 171 A S P E E R K E T 1.500 2109 60M A F D R F V A V 1.200 2110 237 K T K Q I R R A V 1.200 2111 240 Q I RR A V I K I 1.200 2112 190 F A I Y Y I P L I 1.200 2113 118 H S Y C Y HP D V 1.000 2114 19 T L V T M L S I F 1.000 2115 57 L L A M A F D R F1.000 2116 36 F N A C L S H M F 1.000 2117 16 S I S T L V T M L 1.0002118 216 T M I A N T Y L L 1.000 2119 12 D L G L S I S T L 1.000 2120182 T C V S H I V A F 1.000 2121 87 G V A S V I R G L 1.000 2122 220 N TY L L I S P L 1.000 2123 154 L L I L L S Y V L 1.000 2124 7 M L S A T DL G L 1.000 2125 215 H T M I A N T Y L 1.000 2126 96 L M L T P M V A L1.000 2127 97 M L T P M V A L L 1.000 2128 160 Y V L I I R T V L 1.0002129 90 S V I R G L L M L 1.000 2130 180 F S T C V S H I V 1.000 2131 21V T M L S I F W F 1.000 2132 147 S T V G V D L L L 1.000 2133 128 K L SC T D T R I 0.800 2134 129 L S C T D T R I N 0.750 2135 8 L S A T D L GL S 0.750 2136 83 I A Q I G V A S V 0.600 2137 206 F G K Q A P A Y V0.600 2138 243 R A V I K I L H S 0.600 2139 148 T V G V D L L L I 0.6002140 30 N V R E I S F N A 0.600 2141 123 H P D V M K L S C 0.600 2142143 T A M F S T V G V 0.600 2143 58 L A M A F D R F V 0.600 2144 53 E SS V L L A M A 0.500 2145 17 I S T L V T M L S 0.500 2146 20 L V T M L SI F W 0.500 2147 158 L S Y V L I I R T 0.500 2148 98 L T P M V A L L I0.400 2149 107 R L S Y C H S Q V 0.400 2150 217 M I A N T Y L L I 0.4002151 187 I V A F A I Y Y I 0.400 2152 155 L I L L S Y V L I 0.400 215338 A C L S H M F F I 0.400 2154 205 R F G K Q A P A Y 0.400 2155 156 I LL S Y V L I I 0.400 2156 18 S T L V T M L S I 0.400 2157 75 A M I L T DS R I 0.400 2158 84 A Q I G V A S V I 0.400 2159 194 Y I P L I S L S I0.400 2160 69 S N P L R Y A M I 0.400 2161 126 V M K L S C T D T 0.3002162 150 G V D L L L I L L 0.300 2163 163 I I R T V L S V A 0.300 216491 V I R G L L M L T 0.300 2165 105 L I R L S Y C H S 0.300 2166 241 I RR A V I K I L 0.300 2167 218 I A N T Y L L I S 0.300 2168 119 S Y C Y HP D V M 0.200 2169 228 L M N P V I Y S V 0.200 2170 32 R E I S F N A C L0.200 2171 141 G L T A M F S T V 0.200 2172 162 L I I R T V L S V 0.2002173 52 M E S S V L L A M 0.200 2174

TABLE XVII V1B-B35-9mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 61E P M Y Y F L S M 40.000 2175 56 Q P S L H E P M Y 40.000 2176 10 T S TS I I F L L 5.000 2177 21 V P G L E A F H T 3.000 2178 51 F A T I T Q PS L 3.000 2179 46 N S L I L F A T I 2.000 2180 58 S L H E P M Y Y F2.000 2181 33 I P F C F L S V T 2.000 2182 55 T Q P S L H E P M 2.0002183 57 P S L H E P M Y Y 1.500 2184 41 T A L L G N S L I 1.200 2185 25E A F H T W I S I 1.200 2186 30 W I S I P F C F L 1.000 2187 43 L L G NS L I L F 1.000 2188 16 F L L T G V P G L 1.000 2189 19 T G V P G L E AF 1.000 2190 8 N I T S T S I I F 1.000 2191 35 F C F L S V T A L 1.0002192 42 A L L G N S L I L 1.000 2193 40 V T A L L G N S L 1.000 2194 9 IT S T S I I F L 1.000 2195 31 I S I P F C F L S 0.500 2196 3 T S T L Q NI T S 0.500 2197 38 L S V T A L L G N 0.500 2198 7 Q N I T S T S I I0.400 2199 6 L Q N I T S T S I 0.400 2200 1 F I T S T L Q N I 0.400 220132 S I P F C F L S V 0.200 2202 13 S I I F L L T G V 0.200 2203 23 G L EA F H T W I 0.120 2204 44 L G N S L I L F A 0.100 2205 47 S L I L F A TI T 0.100 2206 5 T L Q N I T S T S 0.100 2207 4 S T L Q N I T S T 0.1002208 22 P G L E A F H T W 0.100 2209 11 S T S I I F L L T 0.100 2210 27F H T W I S I P F 0.100 2211 39 S V T A L L G N S 0.100 2212 45 G N S LI L F A T 0.100 2213 18 L T G V P G L E A 0.100 2214 28 H T W I S I P FC 0.100 2215 62 P M Y Y F L S M L 0.100 2216 29 T W I S I P F C F 0.1002217 2 I T S T L Q N I T 0.100 2218 36 C F L S V T A L L 0.100 2219 12 TS I I F L L T G 0.050 2220 59 L H E P M Y Y F L 0.030 2221 54 I T Q P SL H E P 0.010 2222 52 A T I T Q P S L H 0.010 2223 37 F L S V T A L L G0.010 2224 48 L I L F A T I T Q 0.010 2225 14 I I F L L T G V P 0.0102226 20 G V P G L E A F H 0.010 2227 49 I L F A T I T Q P 0.010 2228 50L F A T I T Q P S 0.010 2229 53 T I T Q P S L H E 0.010 2230 17 L L T GV P G L E 0.010 2231 24 L E A F H T W I S 0.010 2232 60 H E P M Y Y F LS 0.010 2233 34 P F C F L S V T A 0.001 2234 15 I F L L T G V P G 0.0012235 26 A F H T W I S I P 0.001 2236 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 00.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000 0 0 0.000

TABLE XVII V2-B35-9mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 Score ID 9 TS P L M N P V I 2.000 2237 4 N T Y L L T S P L 1.000 2238 2 I A N T Y LL T S 0.300 2239 8 L T S P L M N P V 0.200 2240 5 T Y L L T S P L M0.200 2241 6 Y L L T S P L M N 0.100 2242 1 M I A N T Y L L T 0.100 22437 L L T S P L M N P 0.010 2244 3 A N T Y L L T S P 0.010 2245

TABLE XVIII V1-B35-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID99 T P M V A L L I R L 20.000 2246 225 I S P L M N P V I Y 10.000 2247118 H S Y C Y H P D V M 10.000 2248 184 V S H I V A F A I Y 10.000 224934 I S F N A C L S H M 10.000 2250 171 A S P E E R K E T F 10.000 225188 V A S V I R G L L M 6.000 2252 146 F S T V G V D L L L 5.000 2253 89A S V I R G L L M L 5.000 2254 53 E S S V L L A M A F 5.000 2255 137 N SA V G L T A M F 5.000 2256 40 L S H M F F I K F F 5.000 2257 15 L S I ST L V T M L 5.000 2258 208 K Q A P A Y V H T M 4.000 2259 188 V A F A IY Y I P L 3.000 2260 240 Q I R R A V I K I L 3.000 2261 133 D T R I N SA V G L 3.000 2262 237 K T K Q I R R A V I 2.400 2263 14 G L S I S T L VT M 2.000 2264 67 A V S N P L R Y A M 2.000 2265 210 A P A Y V H T M I A2.000 2266 107 R L S Y C H S Q V L 2.000 2267 213 Y V H T M I A N T Y2.000 2268 17 I S T L V T M L S I 2.000 2269 226 S P L M N P V I Y S2.000 2270 113 S Q V L H H S Y C Y 2.000 2271 149 V G V D L L L I L L2.000 2272 70 N P L R Y A M I L T 2.000 2273 220 N T Y L L I S P L M2.000 2274 8 L S A T D L G L S I 2.000 2275 65 F V A V S N P L R Y 2.0002276 136 I N S A V G L T A M 2.000 2277 68 V S N P L R Y A M I 2.0002278 101 M V A L L I R L S Y 2.000 2279 120 Y C Y H P D V M K L 1.5002280 80 D S R I A Q I G V A 1.500 2281 74 Y A M I L T D S R I 1.200 2282172 S P E E R K E T F S 1.200 2283 209 Q A P A Y V H T M I 1.200 2284 37N A C L S H M F F I 1.200 2285 83 I A Q I G V A S V I 1.200 2286 95 L LM L T P M V A L 1.000 2287 20 L V T M L S I F W F 1.000 2288 153 L L L IL L S Y V L 1.000 2289 191 A I Y Y I P L I S L 1.000 2290 144 A M F S TV G V D L 1.000 2291 215 H T M I A N T Y L L 1.000 2292 56 V L L A M A FD R F 1.000 2293 49 F T V M E S S V L L 1.000 2294 4 F L S M L S A T D L1.000 2295 18 S T L V T M L S I F 1.000 2296 219 A N T Y L L I S P L1.000 2297 87 G V A S V I R G L L 1.000 2298 148 T V G V D L L L I L1.000 2299 36 F N A C L S H M F F 1.000 2300 96 L M L T P M V A L L1.000 2301 158 L S Y V L I I R T V 1.000 2302 6 S M L S A T D L G L1.000 2303 69 S N P L R Y A M I L 1.000 2304 86 I G V A S V I R G L1.000 2305 39 C L S H M F F I K F 1.000 2306 197 L I S L S I V H R F1.000 2307 181 S T C V S H I V A F 1.000 2308 77 I L T D S R I A Q I0.800 2309 239 K Q I R R A V I K I 0.800 2310 123 H P D V M K L S C T0.600 2311 9 S A T D L G L S I S 0.600 2312 60 M A F D R F V A V S 0.6002313 51 V M E S S V L L A M 0.600 2314 147 S T V G V D L L L I 0.6002315 30 N V R E I S F N A C 0.600 2316 129 L S C T D T R I N S 0.5002317 180 F S T C V S H I V A 0.500 2318 112 H S Q V L H H S Y C 0.5002319 19 T L V T M L S I F W 0.500 2320 58 L A M A F D R F V A 0.450 2321170 V A S P E E R K E T 0.450 2322 186 H I V A F A I Y Y I 0.400 2323178 E T F S T C V S H I 0.400 2324 216 T M I A N T Y L L I 0.400 2325 93R G L L M L T P M V 0.400 2326 25 S I F W F N V R E I 0.400 2327 154 L LI L L S Y V L I 0.400 2328 97 M L T P M V A L L I 0.400 2329 155 L I L LS Y V L I I 0.400 2330 82 R I A Q I G V A S V 0.400 2331 232 V I Y S V KT K Q I 0.400 2332 183 C V S H I V A F A I 0.400 2333 224 L I S P L M NP V I 0.400 2334 190 F A I Y Y I P L I S 0.300 2335 235 S V K T K Q I RR A 0.300 2336 128 K L S C T D T R I N 0.300 2337 66 V A V S N P L R Y A0.300 2338 45 F I K F F T V M E S 0.300 2339 102 V A L L I R L S Y C0.300 2340 163 I I R T V L S V A S 0.300 2341 245 V I K I L H S K E T0.300 2342 138 S A V G L T A M F S 0.300 2343 142 L T A M F S T V G V0.200 2344 230 N P V I Y S V K T K 0.200 2345

TABLE XVIII V1B-B35-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID56 Q P S L H E P M Y Y 60.000 2346 61 E P M Y Y F L S M L 20.000 2347 21V P G L E A F H T W 10.000 2348 41 T A L L G N S L I L 3.000 2349 58 S LH E P M Y Y F L 2.000 2350 33 I P F C F L S V T A 2.000 2351 54 I T Q PS L H E P M 2.000 2352 55 T Q P S L H E P M Y 2.000 2353 39 S V T A L LG N S L 1.000 2354 8 N I T S T S I I F L 1.000 2355 28 H T W I S I P F CF 1.000 2356 31 I S I P F C F L S V 1.000 2357 35 F C F L S V T A L L1.000 2358 7 Q N I T S T S I I F 1.000 2359 12 T S I I F L L T G V 1.0002360 42 A L L G N S L I L F 1.000 2361 9 I T S T S I I F L L 1.000 236218 L T G V P G L E A F 1.000 2363 57 P S L H E P M Y Y F 0.500 2364 3 TS T L Q N I T S T 0.500 2365 10 T S T S I I F L L T 0.500 2366 38 L S VT A L L G N S 0.500 2367 46 N S L I L F A T I T 0.500 2368 6 L Q N I T ST S I I 0.400 2369 40 V T A L L G N S L I 0.400 2370 45 G N S L I L F AT I 0.400 2371 5 T L Q N I T S T S I 0.400 2372 60 H E P M Y Y F L S M0.200 2373 20 G V P G L E A F H T 0.150 2374 15 I F L L T G V P G L0.100 2375 44 L G N S L I L F A T 0.100 2376 1 F I T S T L Q N I T 0.1002377 32 S I P F C F L S V T 0.100 2378 37 F L S V T A L L G N 0.100 237930 W I S I P F C F L S 0.100 2380 49 I L F A T I T Q P S 0.100 2381 4 ST L Q N I T S T S 0.100 2382 17 L L T G V P G L E A 0.100 2383 50 L F AT I T Q P S L 0.100 2384 43 L L G N S L I L F A 0.100 2385 29 T W I S IP F C F L 0.100 2386 26 A F H T W I S I P F 0.100 2387 2 I T S T L Q N IT S 0.100 2388 22 P G L E A F H T W I 0.080 2389 24 L E A F H T W I S I0.040 2390 51 F A T I T Q P S L H 0.030 2391 25 E A F H T W I S I P0.030 2392 23 G L E A F H T W I S 0.030 2393 34 P F C F L S V T A L0.010 2394 27 F H T W I S I P F C 0.010 2395 19 T G V P G L E A F H0.010 2396 16 F L L T G V P G L E 0.010 2397 48 L I L F A T I T Q P0.010 2398 52 A T I T Q P S L H E 0.010 2399 62 P M Y Y F L S M L S0.010 2400 11 S T S I I F L L T G 0.010 2401 14 I I F L L T G V P G0.010 2402 47 S L I L F A T I T Q 0.010 2403 13 S I I F L L T G V P0.010 2404 53 T I T Q P S L H E P 0.010 2405 59 L H E P M Y Y F L S0.003 2406 36 C F L S V T A L L G 0.001 2407 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 00.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0 0.000

TABLE XVIII V2-B35-10mers: 238P1B2 SEQ Pos 1 2 3 4 5 6 7 8 9 0 Score ID10 T S P L M N P V I Y 10.000 2408 5 N T Y L L T S P L M 2.000 2409 4 AN T Y L L T S P L 1.000 2410 9 L T S P L M N P V I 0.400 2411 8 L L T SP L M N P V 0.200 2412 1 T M I A N T Y L L T 0.100 2413 2 M I A N T Y LL T S 0.100 2414 3 I A N T Y L L T S P 0.030 2415 7 Y L L T S P L M N P0.010 2416 6 T Y L L T S P L M N 0.010 2417

TABLE XIX 238P1B2: HLA Peptide Scoring Results and PositionDetermination Key Variant 1A: for Nonamers, decamers, and 15-mers,search peptide used (SEQ ID: 2418): MYYFLSMLSA TDLGLSISTL VTMLSIFWFNVREISFNACL SHMFFIKFFT VMESSVLLAM AFDRFVAVSN PLRYAMILTD SRIAQIGVASVIRGLLMLTP MVALLIRLSY CHSQVLHHSY CYHPDVMKLS CTDTRINSAV GLTAMFSTVGVDLLLILLSY VLIIRTVLSV ASPEERKETF STCVSHIVAF AIYYIPLISL SIVHRFGPQAPAYVHTMIAN TYLLISPLMN PVIYSVKTKQ IRRAVIKILH SKET Variant 1B: searchpeptides used: Nonamers (aa 1-70) (SEQ ID: 2419) FITSTLQNIT STSIIFLLTGVPGLEAFHTW ISIPFCFLSV TALLGNSLIL FATITQPSLH EPMYYFLSML Decamers (aa1-71) (SEQ ID: 2420) FITSTLQNIT STSIIFLLTG VPGLEAFHTW ISIPFCFLSVTALLGNSLIL FATITQPSLH EPMYYFLSML S 15-mers (aa 1-76) (SEQ ID: 2421)FITSTLQNIT STSIIFLLTG VPGLEAFHTW ISIPFCFLSV TALLGNSLIL FATITQPSLHEPMYYFLSML SATDLG Variant 2: search peptides used: nonamers (aa 217-233)(SEQ ID: 2422) MIANTYLLTSPLMNPVI decamers (aa 216-234) (SEQ ID: 2423)TMIANTYLLTSPLMNPVIY 15-mers for MHC II (aa 211-239) (SEQ ID: 2424)PAYVHTMIANTYLLTSPLMNPVIYSVKTK Note that variant 1A is referred to as“v.1” in the Tables below; variant 1B is referred to as “v.1B” below;variant 2 is referred to as “v.2”.

TABLE XIXA part 1 HLA-A*0201 9-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9score SEQ ID 228 L M N P V I Y S V 30 2425 153 L L L I L L S Y V 29 2426162 L I I R T V L S V 29 2427 156 I L L S Y V L I I 28 2428 94 G L L M LT P M V 27 2429 97 M L T P M V A L L 27 2430 83 I A Q I G V A S V 262431 96 L M L T P M V A L 26 2432 154 L L I L L S Y V L 26 2433 12 D L GL S I S T L 25 2434 16 S I S T L V T M L 25 2435 90 S V I R G L L M L 252436 224 L I S P L M N P V 24 2437 216 T M I A N T Y L L 23 2438 7 M L SA T D L G L 22 2439 87 G V A S V I R G L 22 2440 141 G L T A M F S T V22 2441 155 L I L L S Y V L I 22 2442 240 Q I R R A V I K I 22 2443 23 ML S I F W F N V 21 2444 194 Y I P L I S L S I 21 2445 75 A M I L T D S RI 20 2446 78 L T D S R I A Q I 20 2447 91 V I R G L L M L T 20 2448 100P M V A L L I R L 20 2449 150 G V D L L L I L L 20 2450 187 I V A F A IY Y I 20 2451 190 F A I Y Y I P L I 20 2452 192 I Y Y I P L I S L 202453 220 N T Y L L I S P L 20 2454 18 S T L V T M L S I 19 2455 50 T V ME S S V L L 19 2456 60 M A F D R F V A V 19 2457 107 R L S Y C H S Q V19 2458 128 K L S C T D T R I 19 2459 143 T A M F S T V G V 19 2460 147S T V G V D L L L 19 2461 217 M I A N T Y L L I 19 2462 223 L L I S P LM N P 19 2463 9 S A T D L G L S I 18 2464 14 G L S I S T L V T 18 246558 L A M A F D R F V 18 2466 103 A L L I R L S Y C 18 2467 121 C Y H P DV M K L 18 2468 149 V G V D L L L I L 18 2469 152 D L L L I L L S Y 182470 159 S Y V L I I R T V 18 2471 160 Y V L I I R T V L 18 2472 163 I IR T V L S V A 18 2473 195 I P L I S L S I V 18 2474 51 V M E S S V L L A17 2475 95 L L M L T P M V A 17 2476 135 R I N S A V G L T 17 2477 148 TV G V D L L L I 17 2478 161 V L I I R T V L S 17 2479 4 F L S M L S A TD 16 2480 15 L S I S T L V T M 16 2481 26 I F W F N V R E I 16 2482 104L L I R L S Y C H 16 2483 146 F S T V G V D L L 16 2484 197 L I S L S IV H R 16 2485 209 Q A P A Y V H T M 16 2486 213 Y V H T M I A N T 162487 32 R E I S F N A C L 15 2488 49 F T V M E S S V L 15 2489 59 A M AF D R F V A 15 2490 67 A V S N P L R Y A 15 2491 88 V A S V I R G L L 152492 98 L T P M V A L L I 15 2493 131 C T D T R I N S A 15 2494 134 T RI N S A V G L 15 2495 144 A M F S T V G V D 15 2496 157 L L S Y V L I IR 15 2497 189 A F A I Y Y I P L 15 2498 215 H T M I A N T Y L 15 2499222 Y L L I S P L M N 15 2500 237 K T K Q I R R A V 15 2501 241 I R R AV I K I L 15 2502 244 A V I K I L H S K 15 2503 6 S M L S A T D L G 142504 13 L G L S I S T L V 14 2505 19 T L V T M L S I F 14 2506 25 S I FW F N V R E 14 2507 43 M F F I K F F T V 14 2508 57 L L A M A F D R F 142509 76 M I L T D S R I A 14 2510 84 A Q I G V A S V I 14 2511 167 V L SV A S P E E 14 2512 183 C V S H I V A F A 14 2513 3 Y F L S M L S A T 132514 5 L S M L S A T D L 13 2515 56 V L L A M A F D R 13 2516 70 N P L RY A M I L 13 2517 77 I L T D S R I A Q 13 2518 82 R I A Q I G V A S 132519 108 L S Y C H S Q V L 13 2520 118 H S Y C Y H P D V 13 2521 137 N SA V G L T A M 13 2522 138 S A V G L T A M F 13 2523 218 I A N T Y L L IS 13 2524 227 P L M N P V I Y S 13 2525 10 A T D L G L S I S 12 2526 38A C L S H M F F I 12 2527 42 H M F F I K F F T 12 2528 45 F I K F F T VM E 12 2529 48 F F T V M E S S V 12 2530 69 S N P L R Y A M I 12 2531 74Y A M I L T D S R 12 2532 81 S R I A Q I G V A 12 2533 126 V M K L S C TD T 12 2534 145 M F S T V G V D L 12 2535 158 L S Y V L I I R T 12 2536165 R T V L S V A S P 12 2537 179 T F S T C V S H I 12 2538 199 S L S IV H R F G 12 2539 201 S I V H R F G K Q 12 2540 206 F G K Q A P A Y V 122541 232 V I Y S V K T K Q 12 2542 233 I Y S V K T K Q I 12 2543 11 T DL G L S I S T 11 2544 35 S F N A C L S H M 11 2545 64 R F V A V S N P L11 2546 68 V S N P L R Y A M 11 2547 101 M V A L L I R L S 11 2548 115 VL H H S Y C Y H 11 2549 180 F S T C V S H I V 11 2550 191 A I Y Y I P LI S 11 2551 193 Y Y I P L I S L S 11 2552 208 K Q A P A Y V H T 11 2553210 A P A Y V H T M I 11 2554 225 I S P L M N P V I 11 2555 245 V I K IL H S K E 11 2556 2 Y Y F L S M L S A 10 2557 21 V T M L S I F W F 102558 22 T M L S I F W F N 10 2559 30 N V R E I S F N A 10 2560 39 C L SH M F F I K 10 2561 52 M E S S V L L A M 10 2562 55 S V L L A M A F D 102563 71 P L R Y A M I L T 10 2564 72 L R Y A M I L T D 10 2565 80 D S RI A Q I G V 10 2566 85 Q I G V A S V I R 10 2567 93 R G L L M L T P M 102568 102 V A L L I R L S Y 10 2569 105 L I R L S Y C H S 10 2570 132 T DT R I N S A V 10 2571 176 R K E T F S T C V 10 2572 181 S T C V S H I VA 10 2573 184 V S H I V A F A I 10 2574 196 P L I S L S I V H 10 2575202 I V H R F G K Q A 10 2576 204 H R F G K Q A P A 10 2577 238 T K Q IR R A V I 10 2578 243 R A V I K I L H S 10 2579 61 A F D R F V A V S 92580 136 I N S A V G L T A 9 2581 140 V G L T A M F S T 9 2582 142 L T AM F S T V G 9 2583 151 V D L L L I L L S 9 2584 169 S V A S P E E R K 92585 170 V A S P E E R K E 9 2586 171 A S P E E R K E T 9 2587 186 H I VA F A I Y Y 9 2588 198 I S L S I V H R F 9 2589 230 N P V I Y S V K T 92590 246 I K I L H S K E T 9 2591 8 L S A T D L G L S 8 2592 44 F F I KF F T V M 8 2593 46 I K F F T V M E S 8 2594 53 E S S V L L A M A 8 259565 F V A V S N P L R 8 2596 106 I R L S Y C H S Q 8 2597 211 P A Y V H TM I A 8 2598 236 V K T K Q I R R A 8 2599 89 A S V I R G L L M 7 2600110 Y C H S Q V L H H 7 2601 114 Q V L H H S Y C Y 7 2602 125 D V M K LS C T D 7 2603 182 T C V S H I V A F 7 2604 188 V A F A I Y Y I P 7 2605219 A N T Y L L I S P 7 2606 221 T Y L L I S P L M 7 2607 231 P V I Y SV K T K 7 2608 20 L V T M L S I F W 6 2609 34 I S F N A C L S H 6 261041 S H M F F I K F F 6 2611 66 V A V S N P L R Y 6 2612 73 R Y A M I L TD S 6 2613 86 I G V A S V I R G 6 2614 92 I R G L L M L T P 6 2615 99 TP M V A L L I R 6 2616 120 Y C Y H P D V M K 6 2617 124 P D V M K L S CT 6 2618 127 M K L S C T D T R 6 2619 139 A V G L T A M F S 6 2620 166 TV L S V A S P E 6 2621 178 E T F S T C V S H 6 2622 185 S H I V A F A IY 6 2623 226 S P L M N P V I Y 6 2624 235 S V K T K Q I R R 6 2625 29 FN V R E I S F N 5 2626 36 F N A C L S H M F 5 2627 40 L S H M F F I K F5 2628 111 C H S Q V L H H S 5 2629 119 S Y C Y H P D V M 5 2630 133 D TR I N S A V G 5 2631 164 I R T V L S V A S 5 2632 172 S P E E R K E T F5 2633 174 E E R K E T F S T 5 2634 200 L S I V H R F G K 5 2635 239 K QI R R A V I K 5 2636 24 L S I F W F N V R 4 2637 33 E I S F N A C L S 42638 37 N A C L S H M F F 4 2639 47 K F F T V M E S S 4 2640 54 S S V LL A M A F 4 2641 62 F D R F V A V S N 4 2642 63 D R F V A V S N P 4 2643109 S Y C H S Q V L H 4 2644 112 H S Q V L H H S Y 4 2645 116 L H H S YC Y H P 4 2646 129 L S C T D T R I N 4 2647 168 L S V A S P E E R 4 264817 I S T L V T M L S 3 2649 28 W F N V R E I S F 3 2650 123 H P D V M KL S C 3 2651 203 V H R F G K Q A P 3 2652 207 G K Q A P A Y V H 3 2653212 A Y V H T M I A N 3 2654 214 V H T M I A N T Y 3 2655 27 F W F N V RE I S 2 2656 31 V R E I S F N A C 2 2657 113 S Q V L H H S Y C 2 2658122 Y H P D V M K L S 2 2659 130 S C T D T R I N S 2 2660 205 R F G K QA P A Y 2 2661 234 Y S V K T K Q I R 2 2662 242 R R A V I K I L H 2 26631 M Y Y F L S M L S 1 2664 177 K E T F S T C V S 1 2665 173 P E E R K ET F S −3 2666 HLA-A19-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQID 102 V A L L I R L S Y 23 2667 66 V A V S N P L R Y 22 2668 152 D L LL I L L S Y 22 2669 51 V M E S S V L L A 20 2670 185 S H I V A F A I Y20 2671 10 A T D L G L S I S 19 2672 112 H S Q V L H H S Y 19 2673 147 ST V G V D L L L 19 2674 186 H I V A F A I Y Y 19 2675 205 R F G K Q A PA Y 17 2676 226 S P L M N P V I Y 17 2677 78 L T D S R I A Q I 16 267898 L T P M V A L L I 16 2679 123 H P D V M K L S C 16 2680 131 C T D T RI N S A 16 2681 150 G V D L L L I L L 16 2682 214 V H T M I A N T Y 162683 114 Q V L H H S Y C Y 15 2684 18 S T L V T M L S I 14 2685 31 V R EI S F N A C 14 2686 89 A S V I R G L L M 14 2687 40 L S H M F F I K F 132688 61 A F D R F V A V S 13 2689 181 S T C V S H I V A 13 2690 172 S PE E R K E T F 12 2691 90 S V I R G L L M L 11 2692 110 Y C H S Q V L H H11 2693 34 I S F N A C L S H 10 2694 68 V S N P L R Y A M 10 2695 146 FS T V G V D L L 10 2696 173 P E E R K E T F S 10 2697 176 R K E T F S TC V 10 2698 222 Y L L I S P L M N 10 2699 9 S A T D L G L S I 9 2700 136I N S A V G L T A 9 2701 151 V D L L L I L L S 9 2702 156 I L L S Y V LI I 9 2703 2 Y Y F L S M L S A 8 2704 14 G L S I S T L V T 8 2705 17 I ST L V T M L S 8 2706 24 L S I F W F N V R 8 2707 49 F T V M E S S V L 82708 52 M E S S V L L A M 8 2709 80 D S R I A Q I G V 8 2710 97 M L T PM V A L L 8 2711 148 T V G V D L L L I 8 2712 158 L S Y V L I I R T 82713 193 Y Y I P L I S L S 8 2714 194 Y I P L I S L S I 8 2715 217 M I AN T Y L L I 8 2716 7 M L S A T D L G L 7 2717 21 V T M L S I F W F 72718 71 P L R Y A M I L T 7 2719 121 C Y H P D V M K L 7 2720 130 S C TD T R I N S 7 2721 133 D T R I N S A V G 7 2722 142 L T A M F S T V G 72723 149 V G V D L L L I L 7 2724 157 L L S Y V L I I R 7 2725 162 L I IR T V L S V 7 2726 165 R T V L S V A S P 7 2727 170 V A S P E E R K E 72728 180 F S T C V S H I V 7 2729 184 V S H I V A F A I 7 2730 191 A I YY I P L I S 7 2731 201 S I V H R F G K Q 7 2732 215 H T M I A N T Y L 72733 218 I A N T Y L L I S 7 2734 227 P L M N P V I Y S 7 2735 237 K T KQ I R R A V 7 2736 240 Q I R R A V I K I 7 2737 8 L S A T D L G L S 62738 54 S S V L L A M A F 6 2739 72 L R Y A M I L T D 6 2740 77 I L T DS R I A Q 6 2741 92 I R G L L M L T P 6 2742 99 T P M V A L L I R 6 2743122 Y H P D V M K L S 6 2744 137 N S A V G L T A M 6 2745 171 A S P E ER K E T 6 2746 178 E T F S T C V S H 6 2747 189 A F A I Y Y I P L 6 2748196 P L I S L S I V H 6 2749 220 N T Y L L I S P L 6 2750 225 I S P L MN P V I 6 2751 228 L M N P V I Y S V 6 2752 234 Y S V K T K Q I R 6 2753235 S V K T K Q I R R 6 2754 242 R R A V I K I L H 6 2755 243 R A V I KI L H S 6 2756 11 T D L G L S I S T 5 2757 44 F F I K F F T V M 5 275853 E S S V L L A M A 5 2759 81 S R I A Q I G V A 5 2760 84 A Q I G V A SV I 5 2761 86 I G V A S V I R G 5 2762 108 L S Y C H S Q V L 5 2763 118H S Y C Y H P D V 5 2764 192 I Y Y I P L I S L 5 2765 198 I S L S I V HR F 5 2766 199 S L S I V H R F G 5 2767 200 L S I V H R F G K 5 2768 212A Y V H T M I A N 5 2769 219 A N T Y L L I S P 5 2770 232 V I Y S V K TK Q 5 2771 5 L S M L S A T D L 4 2772 6 S M L S A T D L G 4 2773 15 L SI S T L V T M 4 2774 16 S I S T L V T M L 4 2775 20 L V T M L S I F W 42776 27 F W F N V R E I S 4 2777 28 W F N V R E I S F 4 2778 39 C L S HM F F I K 4 2779 57 L L A M A F D R F 4 2780 65 F V A V S N P L R 4 278188 V A S V I R G L L 4 2782 91 V I R G L L M L T 4 2783 100 P M V A L LI R L 4 2784 109 S Y C H S Q V L H 4 2785 120 Y C Y H P D V M K 4 2786129 L S C T D T R I N 4 2787 138 S A V G L T A M F 4 2788 141 G L T A MF S T V 4 2789 160 Y V L I I R T V L 4 2790 161 V L I I R T V L S 4 2791168 L S V A S P E E R 4 2792 190 F A I Y Y I P L I 4 2793 208 K Q A P AY V H T 4 2794 210 A P A Y V H T M I 4 2795 224 L I S P L M N P V 4 279622 T M L S I F W F N 3 2797 25 S I F W F N V R E 3 2798 43 M F F I K F FT V 3 2799 59 A M A F D R F V A 3 2800 60 M A F D R F V A V 3 2801 62 FD R F V A V S N 3 2802 69 S N P L R Y A M I 3 2803 83 I A Q I G V A S V3 2804 119 S Y C Y H P D V M 3 2805 135 R I N S A V G L T 3 2806 144 A MF S T V G V D 3 2807 145 M F S T V G V D L 3 2808 163 I I R T V L S V A3 2809 169 S V A S P E E R K 3 2810 175 E R K E T F S T C 3 2811 203 V HR F G K Q A P 3 2812 230 N P V I Y S V K T 3 2813 236 V K T K Q I R R A3 2814 245 V I K I L H S K E 3 2815 1 M Y Y F L S M L S 2 2816 3 Y F L SM L S A T 2 2817 4 F L S M L S A T D 2 2818 13 L G L S I S T L V 2 281933 E I S F N A C L S 2 2820 35 S F N A C L S H M 2 2821 36 F N A C L S HM F 2 2822 41 S H M F F I K F F 2 2823 45 F I K F F T V M E 2 2824 47 KF F T V M E S S 2 2825 50 T V M E S S V L L 2 2826 55 S V L L A M A F D2 2827 56 V L L A M A F D R 2 2828 64 R F V A V S N P L 2 2829 67 A V SN P L R Y A 2 2830 74 Y A M I L T D S R 2 2831 87 G V A S V I R G L 22832 94 G L L M L T P M V 2 2833 95 L L M L T P M V A 2 2834 101 M V A LL I R L S 2 2835 103 A L L I R L S Y C 2 2836 111 C H S Q V L H H S 22837 113 S Q V L H H S Y C 2 2838 115 V L H H S Y C Y H 2 2839 154 L L IL L S Y V L 2 2840 155 L I L L S Y V L I 2 2841 159 S Y V L I I R T V 22842 166 T V L S V A S P E 2 2843 167 V L S V A S P E E 2 2844 207 G K QA P A Y V H 2 2845 209 Q A P A Y V H T M 2 2846 213 Y V H T M I A N T 22847 216 T M I A N T Y L L 2 2848 221 T Y L L I S P L M 2 2849 223 L L IS P L M N P 2 2850 238 T K Q I R R A V I 2 2851 241 I R R A V I K I L 22852 12 D L G L S I S T L 1 2853 19 T L V T M L S I F 1 2854 23 M L S IF W F N V 1 2855 26 I F W F N V R E I 1 2856 29 F N V R E I S F N 1 285732 R E I S F N A C L 1 2858 38 A C L S H M F F I 1 2859 46 I K F F T V ME S 1 2860 48 F F T V M E S S V 1 2861 63 D R F V A V S N P 1 2862 70 NP L R Y A M I L 1 2863 75 A M I L T D S R I 1 2864 82 R I A Q I G V A S1 2865 96 L M L T P M V A L 1 2866 104 L L I R L S Y C H 1 2867 106 I RL S Y C H S Q 1 2868 107 R L S Y C H S Q V 1 2869 116 L H H S Y C Y H P1 2870 126 V M K L S C T D T 1 2871 128 K L S C T D T R I 1 2872 132 T DT R I N S A V 1 2873 139 A V G L T A M F S 1 2874 140 V G L T A M F S T1 2875 153 L L L I L L S Y V 1 2876 177 K E T F S T C V S 1 2877 179 T FS T C V S H I 1 2878 183 C V S H I V A F A 1 2879 188 V A F A I Y Y I P1 2880 202 I V H R F G K Q A 1 2881 204 H R F G K Q A P A 1 2882 206 F GK Q A P A Y V 1 2883 229 M N P V I Y S V K 1 2884 231 P V I Y S V K T K1 2885 244 A V I K I L H S K 1 2886 HLA-A26 9-mers v.1: 238P1B2 Pos 1 23 4 5 6 7 8 9 score SEQ ID 152 D L L L I L L S Y 29 2887 12 D L G L S IS T L 28 2888 21 V T M L S I F W F 25 2889 87 G V A S V I R G L 25 289090 S V I R G L L M L 25 2891 16 S I S T L V T M L 24 2892 57 L L A M A FD R F 24 2893 150 G V D L L L I L L 24 2894 220 N T Y L L I S P L 242895 19 T L V T M L S I F 23 2896 97 M L T P M V A L L 23 2897 50 T V ME S S V L L 22 2898 44 F F I K F F T V M 21 2899 178 E T F S T C V S H21 2900 35 S F N A C L S H M 20 2901 114 Q V L H H S Y C Y 20 2902 147 ST V G V D L L L 20 2903 186 H I V A F A I Y Y 20 2904 205 R F G K Q A PA Y 20 2905 49 F T V M E S S V L 19 2906 154 L L I L L S Y V L 19 2907189 A F A I Y Y I P L 19 2908 78 L T D S R I A Q I 18 2909 91 V I R G LL M L T 18 2910 125 D V M K L S C T D 18 2911 160 Y V L I I R T V L 182912 215 H T M I A N T Y L 18 2913 244 A V I K I L H S K 18 2914 7 M L SA T D L G L 17 2915 28 W F N V R E I S F 17 2916 133 D T R I N S A V G17 2917 162 L I I R T V L S V 17 2918 165 R T V L S V A S P 17 2919 182T C V S H I V A F 17 2920 185 S H I V A F A I Y 17 2921 197 L I S L S IV H R 17 2922 223 L L I S P L M N P 17 2923 224 L I S P L M N P V 172924 231 P V I Y S V K T K 17 2925 10 A T D L G L S I S 16 2926 15 L S IS T L V T M 16 2927 33 E I S F N A C L S 16 2928 101 M V A L L I R L S16 2929 105 L I R L S Y C H S 16 2930 121 C Y H P D V M K L 16 2931 131C T D T R I N S A 16 2932 155 L I L L S Y V L I 16 2933 198 I S L S I VH R F 16 2934 213 Y V H T M I A N T 16 2935 18 S T L V T M L S I 15 293640 L S H M F F I K F 15 2937 55 S V L L A M A F D 15 2938 135 R I N S AV G L T 15 2939 138 S A V G L T A M F 15 2940 145 M F S T V G V D L 152941 163 I I R T V L S V A 15 2942 183 C V S H I V A F A 15 2943 187 I VA F A I Y Y I 15 2944 201 S I V H R F G K Q 15 2945 217 M I A N T Y L LI 15 2946 240 Q I R R A V I K I 15 2947 25 S I F W F N V R E 14 2948 41S H M F F I K F F 14 2949 52 M E S S V L L A M 14 2950 63 D R F V A V SN P 14 2951 64 R F V A V S N P L 14 2952 67 A V S N P L R Y A 14 2953 82R I A Q I G V A S 14 2954 96 L M L T P M V A L 14 2955 100 P M V A L L IR L 14 2956 137 N S A V G L T A M 14 2957 148 T V G V D L L L I 14 2958149 V G V D L L L I L 14 2959 153 L L L I L L S Y V 14 2960 175 E R K ET F S T C 14 2961 245 V I K I L H S K E 14 2962 3 Y F L S M L S A T 132963 30 N V R E I S F N A 13 2964 36 F N A C L S H M F 13 2965 43 M F FI K F F T V 13 2966 45 F I K F F T V M E 13 2967 47 K F F T V M E S S 132968 53 E S S V L L A M A 13 2969 54 S S V L L A M A F 13 2970 65 F V AV S N P L R 13 2971 103 A L L I R L S Y C 13 2972 115 V L H H S Y C Y H13 2973 134 T R I N S A V G L 13 2974 141 G L T A M F S T V 13 2975 156I L L S Y V L I I 13 2976 169 S V A S P E E R K 13 2977 192 I Y Y I P LI S L 13 2978 209 Q A P A Y V H T M 13 2979 235 S V K T K Q I R R 132980 237 K T K Q I R R A V 13 2981 32 R E I S F N A C L 12 2982 37 N A CL S H M F F 12 2983 39 C L S H M F F I K 12 2984 61 A F D R F V A V S 122985 66 V A V S N P L R Y 12 2986 68 V S N P L R Y A M 12 2987 71 P L RY A M I L T 12 2988 93 R G L L M L T P M 12 2989 112 H S Q V L H H S Y12 2990 146 F S T V G V D L L 12 2991 157 L L S Y V L I I R 12 2992 166T V L S V A S P E 12 2993 172 S P E E R K E T F 12 2994 179 T F S T C VS H I 12 2995 194 Y I P L I S L S I 12 2996 196 P L I S L S I V H 122997 227 P L M N P V I Y S 12 2998 232 V I Y S V K T K Q 12 2999 241 I RR A V I K I L 12 3000 20 L V T M L S I F W 11 3001 26 I F W F N V R E I11 3002 77 I L T D S R I A Q 11 3003 85 Q I G V A S V I R 11 3004 94 G LL M L T P M V 11 3005 98 L T P M V A L L I 11 3006 102 V A L L I R L S Y11 3007 104 L L I R L S Y C H 11 3008 139 A V G L T A M F S 11 3009 142L T A M F S T V G 11 3010 161 V L I I R T V L S 11 3011 181 S T C V S HI V A 11 3012 202 I V H R F G K Q A 11 3013 226 S P L M N P V I Y 113014 4 F L S M L S A T D 10 3015 76 M I L T D S R I A 10 3016 107 R L SY C H S Q V 10 3017 167 V L S V A S P E E 10 3018 191 A I Y Y I P L I S10 3019 193 Y Y I P L I S L S 10 3020 214 V H T M I A N T Y 10 3021 216T M I A N T Y L L 10 3022 222 Y L L I S P L M N 10 3023 5 L S M L S A TD L 9 3024 14 G L S I S T L V T 9 3025 23 M L S I F W F N V 9 3026 60 MA F D R F V A V 9 3027 70 N P L R Y A M I L 9 3028 95 L L M L T P M V A9 3029 108 L S Y C H S Q V L 9 3030 128 K L S C T D T R I 9 3031 208 K QA P A Y V H T 9 3032 221 T Y L L I S P L M 9 3033 2 Y Y F L S M L S A 83034 46 I K F F T V M E S 8 3035 48 F F T V M E S S V 8 3036 56 V L L AM A F D R 8 3037 88 V A S V I R G L L 8 3038 89 A S V I R G L L M 8 3039119 S Y C Y H P D V M 8 3040 174 E E R K E T F S T 8 3041 199 S L S I VH R F G 8 3042 69 S N P L R Y A M I 7 3043 80 D S R I A Q I G V 7 304481 S R I A Q I G V A 7 3045 110 Y C H S Q V L H H 7 3046 144 A M F S T VG V D 7 3047 190 F A I Y Y I P L I 7 3048 228 L M N P V I Y S V 7 3049236 V K T K Q I R R A 7 3050 24 L S I F W F N V R 6 3051 31 V R E I S FN A C 6 3052 51 V M E S S V L L A 6 3053 83 I A Q I G V A S V 6 3054 86I G V A S V I R G 6 3055 111 C H S Q V L H H S 6 3056 122 Y H P D V M KL S 6 3057 124 P D V M K L S C T 6 3058 158 L S Y V L I I R T 6 3059 188V A F A I Y Y I P 6 3060 195 I P L I S L S I V 6 3061 204 H R F G K Q AP A 6 3062 219 A N T Y L L I S P 6 3063 229 M N P V I Y S V K 6 3064 243R A V I K I L H S 6 3065 8 L S A T D L G L S 5 3066 22 T M L S I F W F N5 3067 29 F N V R E I S F N 5 3068 38 A C L S H M F F I 5 3069 73 R Y AM I L T D S 5 3070 84 A Q I G V A S V I 5 3071 92 I R G L L M L T P 53072 140 V G L T A M F S T 5 3073 151 V D L L L I L L S 5 3074 212 A Y VH T M I A N 5 3075 11 T D L G L S I S T 4 3076 72 L R Y A M I L T D 43077 75 A M I L T D S R I 4 3078 99 T P M V A L L I R 4 3079 117 H H S YC Y H P D 4 3080 159 S Y V L I I R T V 4 3081 171 A S P E E R K E T 43082 218 I A N T Y L L I S 4 3083 9 S A T D L G L S I 3 3084 34 I S F NA C L S H 3 3085 143 T A M F S T V G V 3 3086 164 I R T V L S V A S 33087 170 V A S P E E R K E 3 3088 200 L S I V H R F G K 3 3089 206 F G KQ A P A Y V 3 3090 239 K Q I R R A V I K 3 3091 246 I K I L H S K E T 33092 1 M Y Y F L S M L S 2 3093 27 F W F N V R E I S 2 3094 42 H M F F IK F F T 2 3095 62 F D R F V A V S N 2 3096 74 Y A M I L T D S R 2 3097106 I R L S Y C H S Q 2 3098 109 S Y C H S Q V L H 2 3099 116 L H H S YC Y H P 2 3100 120 Y C Y H P D V M K 2 3101 123 H P D V M K L S C 2 3102126 V M K L S C T D T 2 3103 130 S C T D T R I N S 2 3104 132 T D T R IN S A V 2 3105 168 L S V A S P E E R 2 3106 203 V H R F G K Q A P 2 3107210 A P A Y V H T M I 2 3108 225 I S P L M N P V I 2 3109 230 N P V I YS V K T 2 3110 233 I Y S V K T K Q I 2 3111 234 Y S V K T K Q I R 2 31126 S M L S A T D L G 1 3113 13 L G L S I S T L V 1 3114 17 I S T L V T ML S 1 3115 59 A M A F D R F V A 1 3116 79 T D S R I A Q I G 1 3117 113 SQ V L H H S Y C 1 3118 118 H S Y C Y H P D V 1 3119 127 M K L S C T D TR 1 3120 173 P E E R K E T F S 1 3121 177 K E T F S T C V S 1 3122 184 VS H I V A F A I 1 3123 211 P A Y V H T M I A 1 3124 238 T K Q I R R A VI 1 3125 242 R R A V I K I L H 1 3126 HLA-A3 9-mers v.1: 238P1B2 Pos 1 23 4 5 6 7 8 9 score SEQ ID 239 K Q I R R A V I K 28 3127 244 A V I K I LH S K 28 3128 231 P V I Y S V K T K 27 3129 152 D L L L I L L S Y 243130 90 S V I R G L L M L 23 3131 169 S V A S P E E R K 22 3132 56 V L LA M A F D R 21 3133 82 R I A Q I G V A S 21 3134 103 A L L I R L S Y C21 3135 163 I I R T V L S V A 21 3136 196 P L I S L S I V H 21 3137 202I V H R F G K Q A 21 3138 39 C L S H M F F I K 20 3139 104 L L I R L S YC H 20 3140 107 R L S Y C H S Q V 20 3141 114 Q V L H H S Y C Y 20 3142161 V L I I R T V L S 20 3143 84 A Q I G V A S V I 19 3144 120 Y C Y H PD V M K 19 3145 141 G L T A M F S T V 19 3146 160 Y V L I I R T V L 193147 162 L I I R T V L S V 19 3148 166 T V L S V A S P E 19 3149 186 H IV A F A I Y Y 19 3150 191 A I Y Y I P L I S 19 3151 12 D L G L S I S T L18 3152 14 G L S I S T L V T 18 3153 85 Q I G V A S V I R 18 3154 139 AV G L T A M F S 18 3155 154 L L I L L S Y V L 18 3156 222 Y L L I S P LM N 18 3157 4 F L S M L S A T D 17 3158 19 T L V T M L S I F 17 3159 55S V L L A M A F D 17 3160 95 L L M L T P M V A 17 3161 156 I L L S Y V LI I 17 3162 197 L I S L S I V H R 17 3163 229 M N P V I Y S V K 17 3164235 S V K T K Q I R R 17 3165 97 M L T P M V A L L 16 3166 153 L L L I LL S Y V 16 3167 240 Q I R R A V I K I 16 3168 7 M L S A T D L G L 153169 50 T V M E S S V L L 15 3170 57 L L A M A F D R F 15 3171 65 F V AV S N P L R 15 3172 77 I L T D S R I A Q 15 3173 102 V A L L I R L S Y15 3174 136 I N S A V G L T A 15 3175 155 L I L L S Y V L I 15 3176 157L L S Y V L I I R 15 3177 30 N V R E I S F N A 14 3178 45 F I K F F T VM E 14 3179 67 A V S N P L R Y A 14 3180 91 V I R G L L M L T 14 3181115 V L H H S Y C Y H 14 3182 125 D V M K L S C T D 14 3183 128 K L S CT D T R I 14 3184 194 Y I P L I S L S I 14 3185 200 L S I V H R F G K 143186 205 R F G K Q A P A Y 14 3187 223 L L I S P L M N P 14 3188 226 S PL M N P V I Y 14 3189 232 V I Y S V K T K Q 14 3190 25 S I F W F N V R E13 3191 61 A F D R F V A V S 13 3192 62 F D R F V A V S N 13 3193 71 P LR Y A M I L T 13 3194 72 L R Y A M I L T D 13 3195 94 G L L M L T P M V13 3196 135 R I N S A V G L T 13 3197 148 T V G V D L L L I 13 3198 183C V S H I V A F A 13 3199 185 S H I V A F A I Y 13 3200 187 I V A F A IY Y I 13 3201 199 S L S I V H R F G 13 3202 207 G K Q A P A Y V H 133203 213 Y V H T M I A N T 13 3204 214 V H T M I A N T Y 13 3205 217 M IA N T Y L L I 13 3206 245 V I K I L H S K E 13 3207 34 I S F N A C L S H12 3208 87 G V A S V I R G L 12 3209 89 A S V I R G L L M 12 3210 101 MV A L L I R L S 12 3211 105 L I R L S Y C H S 12 3212 172 S P E E R K ET F 12 3213 201 S I V H R F G K Q 12 3214 15 L S I S T L V T M 11 321516 S I S T L V T M L 11 3216 23 M L S I F W F N V 11 3217 24 L S I F W FN V R 11 3218 33 E I S F N A C L S 11 3219 54 S S V L L A M A F 11 322081 S R I A Q I G V A 11 3221 133 D T R I N S A V G 11 3222 134 T R I N SA V G L 11 3223 138 S A V G L T A M F 11 3224 150 G V D L L L I L L 113225 208 K Q A P A Y V H T 11 3226 224 L I S P L M N P V 11 3227 227 P LM N P V I Y S 11 3228 238 T K Q I R R A V I 11 3229 9 S A T D L G L S I10 3230 20 L V T M L S I F W 10 3231 32 R E I S F N A C L 10 3232 66 V AV S N P L R Y 10 3233 75 A M I L T D S R I 10 3234 76 M I L T D S R I A10 3235 83 I A Q I G V A S V 10 3236 92 I R G L L M L T P 10 3237 127 MK L S C T D T R 10 3238 165 R T V L S V A S P 10 3239 167 V L S V A S PE E 10 3240 178 E T F S T C V S H 10 3241 10 A T D L G L S I S 9 3242 59A M A F D R F V A 9 3243 70 N P L R Y A M I L 9 3244 109 S Y C H S Q V LH 9 3245 175 E R K E T F S T C 9 3246 182 T C V S H I V A F 9 3247 192 IY Y I P L I S L 9 3248 193 Y Y I P L I S L S 9 3249 242 R R A V I K I LH 9 3250 243 R A V I K I L H S 9 3251 18 S T L V T M L S I 8 3252 28 W FN V R E I S F 8 3253 44 F F I K F F T V M 8 3254 60 M A F D R F V A V 83255 69 S N P L R Y A M I 8 3256 78 L T D S R I A Q I 8 3257 93 R G L LM L T P M 8 3258 108 L S Y C H S Q V L 8 3259 112 H S Q V L H H S Y 83260 144 A M F S T V G V D 8 3261 145 M F S T V G V D L 8 3262 195 I P LI S L S I V 8 3263 198 I S L S I V H R F 8 3264 209 Q A P A Y V H T M 83265 220 N T Y L L I S P L 8 3266 241 I R R A V I K I L 8 3267 49 F T VM E S S V L 7 3268 64 R F V A V S N P L 7 3269 74 Y A M I L T D S R 73270 96 L M L T P M V A L 7 3271 98 L T P M V A L L I 7 3272 99 T P M VA L L I R 7 3273 110 Y C H S Q V L H H 7 3274 132 T D T R I N S A V 73275 147 S T V G V D L L L 7 3276 164 I R T V L S V A S 7 3277 168 L S VA S P E E R 7 3278 177 K E T F S T C V S 7 3279 210 A P A Y V H T M I 73280 225 I S P L M N P V I 7 3281 2 Y Y F L S M L S A 6 3282 3 Y F L S ML S A T 6 3283 11 T D L G L S I S T 6 3284 21 V T M L S I F W F 6 328529 F N V R E I S F N 6 3286 35 S F N A C L S H M 6 3287 36 F N A C L S HM F 6 3288 37 N A C L S H M F F 6 3289 43 M F F I K F F T V 6 3290 47 KF F T V M E S S 6 3291 73 R Y A M I L T D S 6 3292 79 T D S R I A Q I G6 3293 106 I R L S Y C H S Q 6 3294 119 S Y C Y H P D V M 6 3295 142 L TA M F S T V G 6 3296 151 V D L L L I L L S 6 3297 159 S Y V L I I R T V6 3298 184 V S H I V A F A I 6 3299 203 V H R F G K Q A P 6 3300 204 H RF G K Q A P A 6 3301 228 L M N P V I Y S V 6 3302 233 I Y S V K T K Q I6 3303 237 K T K Q I R R A V 6 3304 246 I K I L H S K E T 6 3305 1 M Y YF L S M L S 5 3306 5 L S M L S A T D L 5 3307 17 I S T L V T M L S 53308 38 A C L S H M F F I 5 3309 41 S H M F F I K F F 5 3310 48 F F T VM E S S V 5 3311 52 M E S S V L L A M 5 3312 68 V S N P L R Y A M 5 3313113 S Q V L H H S Y C 5 3314 123 H P D V M K L S C 5 3315 137 N S A V GL T A M 5 3316 171 A S P E E R K E T 5 3317 173 P E E R K E T F S 5 3318174 E E R K E T F S T 5 3319 176 R K E T F S T C V 5 3320 181 S T C V SH I V A 5 3321 189 A F A I Y Y I P L 5 3322 206 F G K Q A P A Y V 5 3323211 P A Y V H T M I A 5 3324 216 T M I A N T Y L L 5 3325 218 I A N T YL L I S 5 3326 219 A N T Y L L I S P 5 3327 230 N P V I Y S V K T 5 332840 L S H M F F I K F 4 3329 53 E S S V L L A M A 4 3330 80 D S R I A Q IG V 4 3331 86 I G V A S V I R G 4 3332 118 H S Y C Y H P D V 4 3333 121C Y H P D V M K L 4 3334 124 P D V M K L S C T 4 3335 131 C T D T R I NS A 4 3336 140 V G L T A M F S T 4 3337 143 T A M F S T V G V 4 3338 149V G V D L L L I L 4 3339 158 L S Y V L I I R T 4 3340 212 A Y V H T M IA N 4 3341 234 Y S V K T K Q I R 4 3342 6 S M L S A T D L G 3 3343 13 LG L S I S T L V 3 3344 27 F W F N V R E I S 3 3345 46 I K F F T V M E S3 3346 51 V M E S S V L L A 3 3347 63 D R F V A V S N P 3 3348 126 V M KL S C T D T 3 3349 130 S C T D T R I N S 3 3350 170 V A S P E E R K E 33351 179 T F S T C V S H I 3 3352 190 F A I Y Y I P L I 3 3353 221 T Y LL I S P L M 3 3354 8 L S A T D L G L S 2 3355 22 T M L S I F W F N 23356 26 I F W F N V R E I 2 3357 31 V R E I S F N A C 2 3358 58 L A M AF D R F V 2 3359 88 V A S V I R G L L 2 3360 100 P M V A L L I R L 23361 122 Y H P D V M K L S 2 3362 146 F S T V G V D L L 2 3363 188 V A FA I Y Y I P 2 3364 215 H T M I A N T Y L 2 3365 111 C H S Q V L H H S 13366 180 F S T C V S H I V 1 3367 HLA-B*0702 9-mers v.1: 238P1B2 Pos 1 23 4 5 6 7 8 9 score SEQ ID 70 N P L R Y A M I L 20 3368 210 A P A Y V HT M I 20 3369 230 N P V I Y S V K T 18 3370 195 I P L I S L S I V 173371 96 L M L T P M V A L 16 3372 172 S P E E R K E T F 16 3373 7 M L SA T D L G L 15 3374 145 M F S T V G V D L 15 3375 16 S I S T L V T M L14 3376 147 S T V G V D L L L 14 3377 189 A F A I Y Y I P L 14 3378 192I Y Y I P L I S L 14 3379 241 I R R A V I K I L 14 3380 50 T V M E S S VL L 13 3381 64 R F V A V S N P L 13 3382 67 A V S N P L R Y A 13 3383 88V A S V I R G L L 13 3384 97 M L T P M V A L L 13 3385 99 T P M V A L LI R 13 3386 123 H P D V M K L S C 13 3387 136 I N S A V G L T A 13 3388160 Y V L I I R T V L 13 3389 5 L S M L S A T D L 12 3390 14 G L S I S TL V T 12 3391 32 R E I S F N A C L 12 3392 90 S V I R G L L M L 12 3393121 C Y H P D V M K L 12 3394 134 T R I N S A V G L 12 3395 149 V G V DL L L I L 12 3396 215 H T M I A N T Y L 12 3397 216 T M I A N T Y L L 123398 226 S P L M N P V I Y 12 3399 12 D L G L S I S T L 11 3400 49 F T VM E S S V L 11 3401 52 M E S S V L L A M 11 3402 59 A M A F D R F V A 113403 84 A Q I G V A S V I 11 3404 87 G V A S V I R G L 11 3405 89 A S VI R G L L M 11 3406 100 P M V A L L I R L 11 3407 108 L S Y C H S Q V L11 3408 146 F S T V G V D L L 11 3409 150 G V D L L L I L L 11 3410 154L L I L L S Y V L 11 3411 174 E E R K E T F S T 11 3412 183 C V S H I VA F A 11 3413 208 K Q A P A Y V H T 11 3414 220 N T Y L L I S P L 113415 44 F F I K F F T V M 10 3416 53 E S S V L L A M A 10 3417 60 M A FD R F V A V 10 3418 91 V I R G L L M L T 10 3419 128 K L S C T D T R I10 3420 138 S A V G L T A M F 10 3421 143 T A M F S T V G V 10 3422 156I L L S Y V L I I 10 3423 163 I I R T V L S V A 10 3424 204 H R F G K QA P A 10 3425 224 L I S P L M N P V 10 3426 233 I Y S V K T K Q I 103427 9 S A T D L G L S I 9 3428 38 A C L S H M F F I 9 3429 51 V M E S SV L L A 9 3430 58 L A M A F D R F V 9 3431 68 V S N P L R Y A M 9 343283 I A Q I G V A S V 9 3433 93 R G L L M L T P M 9 3434 107 R L S Y C HS Q V 9 3435 137 N S A V G L T A M 9 3436 148 T V G V D L L L I 9 3437162 L I I R T V L S V 9 3438 171 A S P E E R K E T 9 3439 179 T F S T CV S H I 9 3440 182 T C V S H I V A F 9 3441 217 M I A N T Y L L I 9 3442225 I S P L M N P V I 9 3443 237 K T K Q I R R A V 9 3444 238 T K Q I RR A V I 9 3445 240 Q I R R A V I K I 9 3446 2 Y Y F L S M L S A 8 344711 T D L G L S I S T 8 3448 15 L S I S T L V T M 8 3449 18 S T L V T M LS I 8 3450 23 M L S I F W F N V 8 3451 26 I F W F N V R E I 8 3452 30 NV R E I S F N A 8 3453 41 S H M F F T K F F 8 3454 57 L L A M A F D R F8 3455 71 P L R Y A M I L T 8 3456 75 A M I L T D S R I 8 3457 78 L T DS R I A Q I 8 3458 80 D S R I A Q I G V 8 3459 81 S R I A Q I G V A 83460 94 G L L M L T P M V 8 3461 95 L L M L T P M V A 8 3462 98 L T P MV A L L I 8 3463 135 R I N S A V G L T 8 3464 141 G L T A M F S T V 83465 155 L I L L S Y V L I 8 3466 176 R K E T F S T C V 8 3467 187 I V AF A I Y Y I 8 3468 194 Y I P L I S L S I 8 3469 198 I S L S I V H R F 83470 202 I V H R F G K Q A 8 3471 209 Q A P A Y V H T M 8 3472 3 Y F L SM L S A T 7 3473 13 L G L S I S T L V 7 3474 21 V T M L S I F W F 7 347535 S F N A C L S H M 7 3476 36 F N A C L S H M F 7 3477 37 N A C L S H MF F 7 3478 40 L S H M F F I K F 7 3479 42 H M F F I K F F T 7 3480 43 MF F I K F F T V 7 3481 54 S S V L L A M A F 7 3482 69 S N P L R Y A M I7 3483 118 H S Y C Y H P D V 7 3484 119 S Y C Y H P D V M 7 3485 126 V MK L S C T D T 7 3486 131 C T D T R I N S A 7 3487 132 T D T R I N S A V7 3488 181 S T C V S H I V A 7 3489 184 V S H I V A F A I 7 3490 190 F AI Y Y I P L I 7 3491 206 F G K Q A P A Y V 7 3492 211 P A Y V H T M I A7 3493 213 Y V H T M I A N T 7 3494 221 T Y L L I S P L M 7 3495 228 L MN P V I Y S V 7 3496 236 V K T K Q I R R A 7 3497 246 I K I L H S K E T7 3498 19 T L V T M L S I F 6 3499 28 W F N V R E I S F 6 3500 48 F F TV M E S S V 6 3501 61 A F D R F V A V S 6 3502 76 M I L T D S R I A 63503 82 R I A Q I G V A S 6 3504 124 P D V M K L S C T 6 3505 140 V G LT A M F S T 6 3506 153 L L L I L L S Y V 6 3507 158 L S Y V L I I R T 63508 159 S Y V L I I R T V 6 3509 180 F S T C V S H I V 6 3510 120 Y C YH P D V M K 5 3511 205 R F G K Q A P A Y 5 3512 207 G K Q A P A Y V H 53513 227 P L M N P V I Y S 5 3514 62 F D R F V A V S N 4 3515 92 I R G LL M L T P 4 3516 133 D T R I N S A V G 4 3517 139 A V G L T A M F S 43518 144 A M F S T V G V D 4 3519 164 I R T V L S V A S 4 3520 169 S V AS P E E R K 4 3521 191 A I Y Y I P L I S 4 3522 197 L I S L S I V H R 43523 4 F L S M L S A T D 3 3524 10 A T D L G L S I S 3 3525 33 E I S F NA C L S 3 3526 34 I S F N A C L S H 3 3527 39 C L S H M F F I K 3 352845 F I K F F T V M E 3 3529 72 L R Y A M I L T D 3 3530 73 R Y A M I L TD S 3 3531 77 I L T D S R I A Q 3 3532 85 Q I G V A S V I R 3 3533 86 IG V A S V I R G 3 3534 102 V A L L I R L S Y 3 3535 110 Y C H S Q V L HH 3 3536 117 H H S Y C Y H P D 3 3537 142 L T A M F S T V G 3 3538 161 VL I I R T V L S 3 3539 165 R T V L S V A S P 3 3540 167 V L S V A S P EE 3 3541 170 V A S P E E R K E 3 3542 177 K E T F S T C V S 3 3543 178 ET F S T C V S H 3 3544 199 S L S I V H R F G 3 3545 203 V H R F G K Q AP 3 3546 212 A Y V H T M I A N 3 3547 218 I A N T Y L L I S 3 3548 223 LL I S P L M N P 3 3549 239 K Q I R R A V I K 3 3550 243 R A V I K I L HS 3 3551 244 A V I K I L H S K 3 3552 17 I S T L V T M L S 2 3553 22 T ML S I F W F N 2 3554 24 L S I F W F N V R 2 3555 25 S I F W F N V R E 23556 31 V R E I S F N A C 2 3557 46 I K F F T V M E S 2 3558 55 S V L LA M A F D 2 3559 65 F V A V S N P L R 2 3560 66 V A V S N P L R Y 2 356174 Y A M I L T D S R 2 3562 79 T D S R I A Q I G 2 3563 103 A L L I R LS Y C 2 3564 105 L I R L S Y C H S 2 3565 109 S Y C H S Q V L H 2 3566111 C H S Q V L H H S 2 3567 125 D V M K L S C T D 2 3568 151 V D L L LI L L S 2 3569 152 D L L L I L L S Y 2 3570 157 L L S Y V L I I R 2 3571173 P E E R K E T F S 2 3572 175 E R K E T F S T C 2 3573 185 S H I V AF A I Y 2 3574 219 A N T Y L L I S P 2 3575 222 Y L L I S P L M N 2 3576242 R R A V I K I L H 2 3577 6 S M L S A T D L G 1 3578 8 L S A T D L GL S 1 3579 20 L V T M L S I F W 1 3580 27 F W F N V R E I S 1 3581 29 FN V R E I S F N 1 3582 47 K F F T V M E S S 1 3583 56 V L L A M A F D R1 3584 63 D R F V A V S N P 1 3585 101 M V A L L I R L S 1 3586 106 I RL S Y C H S Q 1 3587 127 M K L S C T D T R 1 3588 129 L S C T D T R I N1 3589 130 S C T D T R I N S 1 3590 166 T V L S V A S P E 1 3591 168 L SV A S P E E R 1 3592 186 H I V A F A I Y Y 1 3593 188 V A F A I Y Y I P1 3594 193 Y Y I P L I S L S 1 3595 196 P L I S L S I V H 1 3596 200 L SI V H R F G K 1 3597 201 S I V H R F G K Q 1 3598 229 M N P V I Y S V K1 3599 231 P V I Y S V K T K 1 3600 232 V I Y S V K T K Q 1 3601 234 Y SV K T K Q I R 1 3602 HLA-B*08 9-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9score SEQ ID 172 S P E E R K E T F 24 3603 235 S V K T K Q I R R 22 3604233 I Y S V K T K Q I 19 3605 241 I R R A V I K I L 19 3606 12 D L G L SI S T L 18 3607 16 S I S T L V T M L 17 3608 69 S N P L R Y A M I 173609 97 M L T P M V A L L 17 3610 154 L L I L L S Y V L 17 3611 240 Q IR R A V I K I 17 3612 7 M L S A T D L G L 16 3613 45 F I K F F T V M E16 3614 70 N P L R Y A M I L 16 3615 88 V A S V I R G L L 16 3616 161 VL I I R T V L S 16 3617 28 W F N V R E I S F 15 3618 78 L T D S R I A QI 15 3619 243 R A V I K I L H S 15 3620 245 V I K I L H S K E 15 3621 60M A F D R F V A V 14 3622 103 A L L I R L S Y C 14 3623 156 I L L S Y VL I I 14 3624 175 E R K E T F S T C 14 3625 201 S I V H R F G K Q 143626 238 T K Q I R R A V I 14 3627 50 T V M E S S V L L 13 3628 71 P L RY A M I L T 13 3629 146 F S T V G V D L L 13 3630 190 F A I Y Y I P L I13 3631 210 A P A Y V H T M I 13 3632 9 S A T D L G L S I 12 3633 19 T LV T M L S I F 12 3634 57 L L A M A F D R F 12 3635 87 G V A S V I R G L12 3636 90 S V I R G L L M L 12 3637 96 L M L T P M V A L 12 3638 126 VM K L S C T D T 12 3639 128 K L S C T D T R I 12 3640 138 S A V G L T AM F 12 3641 147 S T V G V D L L L 12 3642 150 G V D L L L I L L 12 3643155 L I L L S Y V L I 12 3644 215 H T M I A N T Y L 12 3645 220 N T Y LL I S P L 12 3646 5 L S M L S A T D L 11 3647 32 R E I S F N A C L 113648 37 N A C L S H M F F 11 3649 49 F T V M E S S V L 11 3650 91 V I RG L L M L T 11 3651 105 L I R L S Y C H S 11 3652 121 C Y H P D V M K L11 3653 134 T R I N S A V G L 11 3654 145 M F S T V G V D L 11 3655 149V G V D L L L I L 11 3656 163 I I R T V L S V A 11 3657 192 I Y Y I P LI S L 11 3658 194 Y I P L I S L S I 11 3659 204 H R F G K Q A P A 113660 206 F G K Q A P A Y V 11 3661 237 K T K Q I R R A V 11 3662 41 S HM F F I K F F 10 3663 43 M F F I K F F T V 10 3664 54 S S V L L A M A F10 3665 64 R F V A V S N P L 10 3666 100 P M V A L L I R L 10 3667 108 LS Y C H S Q V L 10 3668 124 P D V M K L S C T 10 3669 160 Y V L I I R TV L 10 3670 173 P E E R K E T F S 10 3671 189 A F A I Y Y I P L 10 3672216 T M I A N T Y L L 10 3673 217 M I A N T Y L L I 10 3674 18 S T L V TM L S I 9 3675 21 V T M L S I F W F 9 3676 26 I F W F N V R E I 9 3677131 C T D T R I N S A 9 3678 167 V L S V A S P E E 9 3679 182 T C V S HI V A F 9 3680 225 I S P L M N P V I 9 3681 226 S P L M N P V I Y 9 3682239 K Q I R R A V I K 9 3683 25 S I F W F N V R E 8 3684 30 N V R E I SF N A 8 3685 62 F D R F V A V S N 8 3686 77 I L T D S R I A Q 8 3687 89A S V I R G L L M 8 3688 123 H P D V M K L S C 8 3689 174 E E R K E T FS T 8 3690 184 V S H I V A F A I 8 3691 187 I V A F A I Y Y I 8 3692 198I S L S I V H R F 8 3693 199 S L S I V H R F G 8 3694 203 V H R F G K QA P 8 3695 4 F L S M L S A T D 7 3696 14 G L S I S T L V T 7 3697 36 F NA C L S H M F 7 3698 56 V L L A M A F D R 7 3699 75 A M I L T D S R I 73700 94 G L L M L T P M V 7 3701 95 L L M L T P M V A 7 3702 99 T P M VA L L I R 7 3703 107 R L S Y C H S Q V 7 3704 115 V L H H S Y C Y H 73705 141 G L T A M F S T V 7 3706 148 T V G V D L L L I 7 3707 152 D L LL I L L S Y 7 3708 157 L L S Y V L I I R 7 3709 179 T F S T C V S H I 73710 195 I P L I S L S I V 7 3711 197 L I S L S I V H R 7 3712 227 P L MN P V I Y S 7 3713 230 N P V I Y S V K T 7 3714 23 M L S I F W F N V 63715 33 E I S F N A C L S 6 3716 38 A C L S H M F F I 6 3717 39 C L S HM F F I K 6 3718 40 L S H M F F I K F 6 3719 80 D S R I A Q I G V 6 372082 R I A Q I G V A S 6 3721 83 I A Q I G V A S V 6 3722 84 A Q I G V A SV I 6 3723 85 Q I G V A S V I R 6 3724 98 L T P M V A L L I 6 3725 102 VA L L I R L S Y 6 3726 104 L L I R L S Y C H 6 3727 133 D T R I N S A VG 6 3728 153 L L L I L L S Y V 6 3729 196 P L I S L S I V H 6 3730 222 YL L I S P L M N 6 3731 223 L L I S P L M N P 6 3732 66 V A V S N P L R Y5 3733 135 R I N S A V G L T 5 3734 143 T A M F S T V G V 5 3735 162 L II R T V L S V 5 3736 170 V A S P E E R K E 5 3737 186 H I V A F A I Y Y5 3738 188 V A F A I Y Y I P 5 3739 191 A I Y Y I P L I S 5 3740 209 Q AP A Y V H T M 5 3741 211 P A Y V H T M I A 5 3742 218 I A N T Y L L I S5 3743 232 V I Y S V K T K Q 5 3744 58 L A M A F D R F V 4 3745 74 Y A MI L T D S R 4 3746 76 M I L T D S R I A 4 3747 159 S Y V L I I R T V 43748 164 I R T V L S V A S 4 3749 171 A S P E E R K E T 4 3750 224 L I SP L M N P V 4 3751 246 I K I L H S K E T 4 3752 46 I K F F T V M E S 33753 53 E S S V L L A M A 3 3754 55 S V L L A M A F D 3 3755 65 F V A VS N P L R 3 3756 81 S R I A Q I G V A 3 3757 109 S Y C H S Q V L H 33758 113 S Q V L H H S Y C 3 3759 119 S Y C Y H P D V M 3 3760 151 V D LL L I L L S 3 3761 178 E T F S T C V S H 3 3762 181 S T C V S H I V A 33763 185 S H I V A F A I Y 3 3764 231 P V I Y S V K T K 3 3765 6 S M L SA T D L G 2 3766 17 I S T L V T M L S 2 3767 29 F N V R E I S F N 2 376831 V R E I S F N A C 2 3769 35 S F N A C L S H M 2 3770 48 F F T V M E SS V 2 3771 51 V M E S S V L L A 2 3772 63 D R F V A V S N P 2 3773 68 VS N P L R Y A M 2 3774 86 I G V A S V I R G 2 3775 92 I R G L L M L T P2 3776 101 M V A L L I R L S 2 3777 112 H S Q V L H H S Y 2 3778 117 H HS Y C Y H P D 2 3779 130 S C T D T R I N S 2 3780 132 T D T R I N S A V2 3781 137 N S A V G L T A M 2 3782 158 L S Y V L I I R T 2 3783 165 R TV L S V A S P 2 3784 169 S V A S P E E R K 2 3785 202 I V H R F G K Q A2 3786 236 V K T K Q I R R A 2 3787 2 Y Y F L S M L S A 1 3788 3 Y F L SM L S A T 1 3789 10 A T D L G L S I S 1 3790 15 L S I S T L V T M 1 379127 F W F N V R E I S 1 3792 34 I S F N A C L S H 1 3793 42 H M F F I K FF T 1 3794 44 F F I K F F T V M 1 3795 52 M E S S V L L A M 1 3796 61 AF D R F V A V S 1 3797 72 L R Y A M I L T D 1 3798 93 R G L L M L T P M1 3799 106 I R L S Y C H S Q 1 3800 110 Y C H S Q V L H H 1 3801 118 H SY C Y H P D V 1 3802 120 Y C Y H P D V M K 1 3803 122 Y H P D V M K L S1 3804 136 I N S A V G L T A 1 3805 139 A V G L T A M F S 1 3806 140 V GL T A M F S T 1 3807 144 A M F S T V G V D 1 3808 168 L S V A S P E E R1 3809 180 F S T C V S H I V 1 3810 183 C V S H I V A F A 1 3811 193 Y YI P L I S L S 1 3812 200 L S I V H R F G K 1 3813 205 R F G K Q A P A Y1 3814 207 G K Q A P A Y V H 1 3815 208 K Q A P A Y V H T 1 3816 212 A YV H T M I A N 1 3817 213 Y V H T M I A N T 1 3818 214 V H T M I A N T Y1 3819 219 A N T Y L L I S P 1 3820 221 T Y L L I S P L M 1 3821 228 L MN P V I Y S V 1 3822 229 M N P V I Y S V K 1 3823 242 R R A V I K I L H1 3824 HLA-B*1510 9-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID41 S H M F F I K F F 17 3825 87 G V A S V I R G L 15 3826 96 L M L T P MV A L 15 3827 50 T V M E S S V L L 14 3828 160 Y V L I I R T V L 14 382988 V A S V I R G L L 13 3830 97 M L T P M V A L L 13 3831 121 C Y H P DV M K L 13 3832 122 Y H P D V M K L S 13 3833 134 T R I N S A V G L 133834 145 M F S T V G V D L 13 3835 146 F S T V G V D L L 13 3836 192 I YY I P L I S L 13 3837 203 V H R F G K Q A P 13 3838 241 I R R A V I K IL 13 3839 12 D L G L S I S T L 12 3840 16 S I S T L V T M L 12 3841 49 FT V M E S S V L 12 3842 100 P M V A L L I R L 12 3843 108 L S Y C H S QV L 12 3844 111 C H S Q V L H H S 12 3845 154 L L I L L S Y V L 12 3846216 T M I A N T Y L L 12 3847 7 M L S A T D L G L 11 3848 90 S V I R G LL M L 11 3849 117 H H S Y C Y H P D 11 3850 147 S T V G V D L L L 113851 149 V G V D L L L I L 11 3852 150 G V D L L L I L L 11 3853 182 T CV S H I V A F 11 3854 185 S H I V A F A I Y 11 3855 189 A F A I Y Y I PL 11 3856 198 I S L S I V H R F 11 3857 214 V H T M I A N T Y 11 3858220 N T Y L L I S P L 11 3859 5 L S M L S A T D L 10 3860 32 R E I S F NA C L 10 3861 64 R F V A V S N P L 10 3862 68 V S N P L R Y A M 10 386370 N P L R Y A M I L 10 3864 116 L H H S Y C Y H P 10 3865 137 N S A V GL T A M 10 3866 172 S P E E R K E T F 10 3867 215 H T M I A N T Y L 103868 15 L S I S T L V T M 9 3869 44 F F I K F F T V M 9 3870 57 L L A MA F D R F 9 3871 119 S Y C Y H P D V M 9 3872 52 M E S S V L L A M 83873 209 Q A P A Y V H T M 8 3874 221 T Y L L I S P L M 8 3875 19 T L VT M L S I F 7 3876 21 V T M L S I F W F 7 3877 26 I F W F N V R E I 73878 28 W F N V R E I S F 7 3879 36 F N A C L S H M F 7 3880 54 S S V LL A M A F 7 3881 138 S A V G L T A M F 7 3882 35 S F N A C L S H M 63883 37 N A C L S H M F F 6 3884 40 L S H M F F I K F 6 3885 89 A S V IR G L L M 6 3886 93 R G L L M L T P M 6 3887 164 I R T V L S V A S 63888 236 V K T K Q I R R A 6 3889 77 I L T D S R I A Q 5 3890 82 R I A QI G V A S 5 3891 86 I G V A S V I R G 5 3892 170 V A S P E E R K E 53893 208 K Q A P A Y V H T 5 3894 225 I S P L M N P V I 5 3895 237 K T KQ I R R A V 5 3896 14 G L S I S T L V T 4 3897 25 S I F W F N V R E 43898 46 I K F F T V M E S 4 3899 59 A M A F D R F V A 4 3900 60 M A F DR F V A V 4 3901 66 V A V S N P L R Y 4 3902 67 A V S N P L R Y A 4 390383 I A Q I G V A S V 4 3904 92 I R G L L M L T P 4 3905 101 M V A L L IR L S 4 3906 120 Y C Y H P D V M K 4 3907 136 I N S A V G L T A 4 3908158 L S Y V L I I R T 4 3909 159 S Y V L I I R T V 4 3910 163 I I R T VL S V A 4 3911 167 V L S V A S P E E 4 3912 169 S V A S P E E R K 4 3913187 I V A F A I Y Y I 4 3914 193 Y Y I P L I S L S 4 3915 197 L I S L SI V H R 4 3916 207 G K Q A P A Y V H 4 3917 224 L I S P L M N P V 4 3918226 S P L M N P V I Y 4 3919 233 I Y S V K T K Q I 4 3920 238 T K Q I RR A V I 4 3921 33 E I S F N A C L S 3 3922 53 E S S V L L A M A 3 392361 A F D R F V A V S 3 3924 65 F V A V S N P L R 3 3925 81 S R I A Q I GV A 3 3926 84 A Q I G V A S V I 3 3927 85 Q I G V A S V I R 3 3928 95 LL M L T P M V A 3 3929 128 K L S C T D T R I 3 3930 133 D T R I N S A VG 3 3931 142 L T A M F S T V G 3 3932 143 T A M F S T V G V 3 3933 144 AM F S T V G V D 3 3934 156 I L L S Y V L I I 3 3935 171 A S P E E R K ET 3 3936 175 E R K E T F S T C 3 3937 178 E T F S T C V S H 3 3938 179 TF S T C V S H I 3 3939 181 S T C V S H I V A 3 3940 199 S L S I V H R FG 3 3941 205 R F G K Q A P A Y 3 3942 228 L M N P V I Y S V 3 3943 229 MN P V I Y S V K 3 3944 234 Y S V K T K Q I R 3 3945 242 R R A V I K I LH 3 3946 246 I K I L H S K E T 3 3947 2 Y Y F L S M L S A 2 3948 3 Y F LS M L S A T 2 3949 4 F L S M L S A T D 2 3950 11 T D L G L S I S T 23951 17 I S T L V T M L S 2 3952 18 S T L V T M L S I 2 3953 24 L S I FW F N V R 2 3954 31 V R E I S F N A C 2 3955 34 I S F N A C L S H 2 395645 F I K F F T V M E 2 3957 51 V M E S S V L L A 2 3958 58 L A M A F D RF V 2 3959 62 F D R F V A V S N 2 3960 63 D R F V A V S N P 2 3961 72 LR Y A M I L T D 2 3962 75 A M I L T D S R I 2 3963 76 M I L T D S R I A2 3964 79 T D S R I A Q I G 2 3965 94 G L L M L T P M V 2 3966 99 T P MV A L L I R 2 3967 106 I R L S Y C H S Q 2 3968 109 S Y C H S Q V L H 23969 110 Y C H S Q V L H H 2 3970 123 H P D V M K L S C 2 3971 125 D V MK L S C T D 2 3972 129 L S C T D T R I N 2 3973 130 S C T D T R I N S 23974 132 T D T R I N S A V 2 3975 141 G L T A M F S T V 2 3976 148 T V GV D L L L I 2 3977 155 L I L L S Y V L I 2 3978 161 V L I I R T V L S 23979 168 L S V A S P E E R 2 3980 174 E E R K E T F S T 2 3981 177 K E TF S T C V S 2 3982 183 C V S H I V A F A 2 3983 190 F A I Y Y I P L I 23984 195 I P L I S L S I V 2 3985 196 P L I S L S I V H 2 3986 200 L S IV H R F G K 2 3987 202 I V H R F G K Q A 2 3988 206 F G K Q A P A Y V 23989 212 A Y V H T M I A N 2 3990 213 Y V H T M I A N T 2 3991 218 I A NT Y L L I S 2 3992 222 Y L L I S P L M N 2 3993 227 P L M N P V I Y S 23994 230 N P V I Y S V K T 2 3995 231 P V I Y S V K T K 2 3996 235 S V KT K Q I R R 2 3997 239 K Q I R R A V I K 2 3998 8 L S A T D L G L S 13999 9 S A T D L G L S I 1 4000 10 A T D L G L S I S 1 4001 22 T M L S IF W F N 1 4002 23 M L S I F W F N V 1 4003 27 F W F N V R E I S 1 400429 F N V R E I S F N 1 4005 30 N V R E I S F N A 1 4006 38 A C L S H M FF I 1 4007 39 C L S H M F F I K 1 4008 42 H M F F I K F F T 1 4009 43 MF F I K F F T V 1 4010 47 K F F T V M E S S 1 4011 48 F F T V M E S S V1 4012 55 S V L L A M A F D 1 4013 71 P L R Y A M I L T 1 4014 73 R Y AM I L T D S 1 4015 74 Y A M I L T D S R 1 4016 78 L T D S R I A Q I 14017 91 V I R G L L M L T 1 4018 102 V A L L I R L S Y 1 4019 107 R L SY C H S Q V 1 4020 112 H S Q V L H H S Y 1 4021 118 H S Y C Y H P D V 14022 127 M K L S C T D T R 1 4023 131 C T D T R I N S A 1 4024 135 R I NS A V G L T 1 4025 140 V G L T A M F S T 1 4026 151 V D L L L I L L S 14027 157 L L S Y V L I I R 1 4028 162 L I I R T V L S V 1 4029 165 R T VL S V A S P 1 4030 166 T V L S V A S P E 1 4031 173 P E E R K E T F S 14032 176 R K E T F S T C V 1 4033 184 V S H I V A F A I 1 4034 191 A I YY I P L I S 1 4035 194 Y I P L I S L S I 1 4036 204 H R F G K Q A P A 14037 210 A P A Y V H T M I 1 4038 211 P A Y V H T M I A 1 4039 217 M I AN T Y L L I 1 4040 223 L L I S P L M N P 1 4041 232 V I Y S V K T K Q 14042 240 Q I R R A V I K I 1 4043 243 R A V I K I L H S 1 4044 244 A V IK I L H S K 1 4045 HLA-B*2705 9-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9score SEQ ID 134 T R I N S A V G L 25 4046 241 I R R A V I K I L 25 4047242 R R A V I K I L H 25 4048 204 H R F G K Q A P A 19 4049 32 R E I S FN A C L 18 4050 64 R F V A V S N P L 18 4051 93 R G L L M L T P M 184052 220 N T Y L L I S P L 18 4053 244 A V I K I L H S K 18 4054 12 D LG L S I S T L 17 4055 63 D R F V A V S N P 17 4056 72 L R Y A M I L T D17 4057 87 G V A S V I R G L 17 4058 150 G V D L L L I L L 17 4059 154 LL I L L S Y V L 17 4060 192 I Y Y I P L I S L 17 4061 198 I S L S I V HR F 17 4062 81 S R I A Q I G V A 16 4063 90 S V I R G L L M L 16 4064100 P M V A L L I R L 16 4065 147 S T V G V D L L L 16 4066 160 Y V L II R T V L 16 4067 197 L I S L S I V H R 16 4068 205 R F G K Q A P A Y 164069 235 S V K T K Q I R R 16 4070 239 K Q I R R A V I K 16 4071 5 L S ML S A T D L 15 4072 21 V T M L S I F W F 15 4073 44 F F I K F F T V M 154074 49 F T V M E S S V L 15 4075 54 S S V L L A M A F 15 4076 84 A Q IG V A S V I 15 4077 92 I R G L L M L T P 15 4078 120 Y C Y H P D V M K15 4079 121 C Y H P D V M K L 15 4080 138 S A V G L T A M F 15 4081 152D L L L I L L S Y 15 4082 182 T C V S H I V A F 15 4083 207 G K Q A P AY V H 15 4084 231 P V I Y S V K T K 15 4085 16 S I S T L V T M L 14 408624 L S I F W F N V R 14 4087 34 I S F N A C L S H 14 4088 50 T V M E S SV L L 14 4089 70 N P L R Y A M I L 14 4090 75 A M I L T D S R I 14 409196 L M L T P M V A L 14 4092 102 V A L L I R L S Y 14 4093 106 I R L S YC H S Q 14 4094 108 L S Y C H S Q V L 14 4095 149 V G V D L L L I L 144096 164 I R T V L S V A S 14 4097 196 P L I S L S I V H 14 4098 221 T YL L I S P L M 14 4099 234 Y S V K T K Q I R 14 4100 15 L S I S T L V T M13 4101 19 T L V T M L S I F 13 4102 37 N A C L S H M F F 13 4103 40 L SH M F F I K F 13 4104 41 S H M F F I K F F 13 4105 56 V L L A M A F D R13 4106 65 F V A V S N P L R 13 4107 97 M L T P M V A L L 13 4108 104 LL I R L S Y C H 13 4109 127 M K L S C T D T R 13 4110 128 K L S C T D TR I 13 4111 137 N S A V G L T A M 13 4112 146 F S T V G V D L L 13 4113157 L L S Y V L I I R 13 4114 168 L S V A S P E E R 13 4115 169 S V A SP E E R K 13 4116 172 S P E E R K E T F 13 4117 175 E R K E T F S T C 134118 178 E T F S T C V S H 13 4119 215 H T M I A N T Y L 13 4120 216 T MI A N T Y L L 13 4121 229 M N P V I Y S V K 13 4122 7 M L S A T D L G L12 4123 28 W F N V R E I S F 12 4124 31 V R E I S F N A C 12 4125 36 F NA C L S H M F 12 4126 57 L L A M A F D R F 12 4127 66 V A V S N P L R Y12 4128 74 Y A M I L T D S R 12 4129 85 Q I G V A S V I R 12 4130 99 T PM V A L L I R 12 4131 109 S Y C H S Q V L H 12 4132 114 Q V L H H S Y CY 12 4133 145 M F S T V G V D L 12 4134 189 A F A I Y Y I P L 12 4135190 F A I Y Y I P L I 12 4136 200 L S I V H R F G K 12 4137 214 V H T MI A N T Y 12 4138 52 M E S S V L L A M 11 4139 68 V S N P L R Y A M 114140 78 L T D S R I A Q I 11 4141 88 V A S V I R G L L 11 4142 89 A S VI R G L L M 11 4143 155 L I L L S Y V L I 11 4144 156 I L L S Y V L I I11 4145 185 S H I V A F A I Y 11 4146 186 H I V A F A I Y Y 11 4147 187I V A F A I Y Y I 11 4148 194 Y I P L I S L S I 11 4149 225 I S P L M NP V I 11 4150 226 S P L M N P V I Y 11 4151 18 S T L V T M L S I 10 415235 S F N A C L S H M 10 4153 39 C L S H M F F I K 10 4154 110 Y C H S QV L H H 10 4155 112 H S Q V L H H S Y 10 4156 165 R T V L S V A S P 104157 209 Q A P A Y V H T M 10 4158 210 A P A Y V H T M I 10 4159 240 Q IR R A V I K I 10 4160 243 R A V I K I L H S 10 4161 9 S A T D L G L S I9 4162 26 I F W F N V R E I 9 4163 38 A C L S H M F F I 9 4164 98 L T PM V A L L I 9 4165 115 V L H H S Y C Y H 9 4166 119 S Y C Y H P D V M 94167 158 L S Y V L I I R T 9 4168 233 I Y S V K T K Q I 9 4169 11 T D LG L S I S T 8 4170 69 S N P L R Y A M I 8 4171 73 R Y A M I L T D S 84172 82 R I A Q I G V A S 8 4173 148 T V G V D L L L I 8 4174 151 V D LL L I L L S 8 4175 179 T F S T C V S H I 8 4176 184 V S H I V A F A I 84177 193 Y Y I P L I S L S 8 4178 232 V I Y S V K T K Q 8 4179 238 T K QI R R A V I 8 4180 2 Y Y F L S M L S A 7 4181 25 S I F W F N V R E 74182 46 I K F F T V M E S 7 4183 47 K F F T V M E S S 7 4184 86 I G V AS V I R G 7 4185 94 G L L M L T P M V 7 4186 159 S Y V L I I R T V 74187 176 R K E T F S T C V 7 4188 217 M I A N T Y L L I 7 4189 223 L L IS P L M N P 7 4190 228 L M N P V I Y S V 7 4191 236 V K T K Q I R R A 74192 10 A T D L G L S I S 6 4193 13 L G L S I S T L V 6 4194 14 G L S IS T L V T 6 4195 29 F N V R E I S F N 6 4196 83 I A Q I G V A S V 6 4197107 R L S Y C H S Q V 6 4198 144 A M F S T V G V D 6 4199 195 I P L I SL S I V 6 4200 213 Y V H T M I A N T 6 4201 246 I K I L H S K E T 6 42021 M Y Y F L S M L S 5 4203 30 N V R E I S F N A 5 4204 42 H M F F I K FF T 5 4205 43 M F F I K F F T V 5 4206 91 V I R G L L M L T 5 4207 101 MV A L L I R L S 5 4208 103 A L L I R L S Y C 5 4209 125 D V M K L S C TD 5 4210 131 C T D T R I N S A 5 4211 135 R I N S A V G L T 5 4212 141 GL T A M F S T V 5 4213 153 L L L I L L S Y V 5 4214 162 L I I R T V L SV 5 4215 163 I I R T V L S V A 5 4216 166 T V L S V A S P E 5 4217 188 VA F A I Y Y I P 5 4218 191 A I Y Y I P L I S 5 4219 219 A N T Y L L I SP 5 4220 230 N P V I Y S V K T 5 4221 237 K T K Q I R R A V 5 4222 3 Y FL S M L S A T 4 4223 4 F L S M L S A T D 4 4224 17 I S T L V T M L S 44225 22 T M L S I F W F N 4 4226 27 F W F N V R E I S 4 4227 55 S V L LA M A F D 4 4228 60 M A F D R F V A V 4 4229 61 A F D R F V A V S 4 423062 F D R F V A V S N 4 4231 111 C H S Q V L H H S 4 4232 124 P D V M K LS C T 4 4233 126 V M K L S C T D T 4 4234 136 I N S A V G L T A 4 4235139 A V G L T A M F S 4 4236 142 L T A M F S T V G 4 4237 170 V A S P EE R K E 4 4238 171 A S P E E R K E T 4 4239 174 E E R K E T F S T 4 4240177 K E T F S T C V S 4 4241 208 K Q A P A Y V H T 4 4242 222 Y L L I SP L M N 4 4243 245 V I K I L H S K E 4 4244 20 L V T M L S I F W 3 424551 V M E S S V L L A 3 4246 53 E S S V L L A M A 3 4247 67 A V S N P L RY A 3 4248 76 M I L T D S R I A 3 4249 77 I L T D S R I A Q 3 4250 80 DS R I A Q I G V 3 4251 95 L L M L T P M V A 3 4252 113 S Q V L H H S Y C3 4253 118 H S Y C Y H P D V 3 4254 123 H P D V M K L S C 3 4255 130 S CT D T R I N S 3 4256 132 T D T R I N S A V 3 4257 133 D T R I N S A V G3 4258 140 V G L T A M F S T 3 4259 161 V L I I R T V L S 3 4260 167 V LS V A S P E E 3 4261 173 P E E R K E T F S 3 4262 181 S T C V S H I V A3 4263 183 C V S H I V A F A 3 4264 201 S I V H R F G K Q 3 4265 203 V HR F G K Q A P 3 4266 206 F G K Q A P A Y V 3 4267 211 P A Y V H T M I A3 4268 212 A Y V H T M I A N 3 4269 218 I A N T Y L L I S 3 4270 224 L IS P L M N P V 3 4271 227 P L M N P V I Y S 3 4272 6 S M L S A T D L G 24273 23 M L S I F W F N V 2 4274 48 F F T V M E S S V 2 4275 59 A M A FD R F V A 2 4276 79 T D S R I A Q I G 2 4277 105 L I R L S Y C H S 24278 143 T A M F S T V G V 2 4279 180 F S T C V S H I V 2 4280 202 I V HR F G K Q A 2 4281 8 L S A T D L G L S 1 4282 33 E I S F N A C L S 14283 45 F I K F F T V M E 1 4284 58 L A M A F D R F V 1 4285 71 P L R YA M I L T 1 4286 116 L H H S Y C Y H P 1 4287 122 Y H P D V M K L S 14288 199 S L S I V H R F G 1 4289 HLA-B*2709 9-mers v.1: 238P1B2 Pos 1 23 4 5 6 7 8 9 score SEQ ID 134 T R I N S A V G L 23 4290 241 I R R A V IK I L 21 4291 32 R E I S F N A C L 16 4292 64 R F V A V S N P L 15 4293198 I S L S I V H R F 15 4294 242 R R A V I K I L H 15 4295 63 D R F V AV S N P 14 4296 87 G V A S V I R G L 14 4297 93 R G L L M L T P M 144298 94 G L L M L T P M V 14 4299 106 I R L S Y C H S Q 14 4300 156 I LL S Y V L I I 14 4301 70 N P L R Y A M I L 13 4302 72 L R Y A M I L T D13 4303 96 L M L T P M V A L 13 4304 97 M L T P M V A L L 13 4305 107 RL S Y C H S Q V 13 4306 121 C Y H P D V M K L 13 4307 150 G V D L L L IL L 13 4308 160 Y V L I I R T V L 13 4309 164 I R T V L S V A S 13 4310192 I Y Y I P L I S L 13 4311 13 L G L S I S T L V 12 4312 38 A C L S HM F F I 12 4313 90 S V I R G L L M L 12 4314 92 I R G L L M L T P 124315 100 P M V A L L I R L 12 4316 108 L S Y C H S Q V L 12 4317 141 G LT A M F S T V 12 4318 146 F S T V G V D L L 12 4319 147 S T V G V D L LL 12 4320 149 V G V D L L L I L 12 4321 154 L L I L L S Y V L 12 4322176 R K E T F S T C V 12 4323 204 H R F G K Q A P A 12 4324 216 T M I AN T Y L L 12 4325 220 N T Y L L I S P L 12 4326 221 T Y L L I S P L M 124327 5 L S M L S A T D L 11 4328 7 M L S A T D L G L 11 4329 15 L S I ST L V T M 11 4330 16 S I S T L V T M L 11 4331 18 S T L V T M L S I 114332 49 F T V M E S S V L 11 4333 50 T V M E S S V L L 11 4334 60 M A FD R F V A V 11 4335 75 A M I L T D S R I 11 4336 81 S R I A Q I G V A 114337 84 A Q I G V A S V I 11 4338 88 V A S V I R G L L 11 4339 89 A S VI R G L L M 11 4340 118 H S Y C Y H P D V 11 4341 128 K L S C T D T R I11 4342 145 M F S T V G V D L 11 4343 155 L I L L S Y V L I 11 4344 162L I I R T V L S V 11 4345 182 T C V S H I V A F 11 4346 189 A F A I Y YI P L 11 4347 195 I P L I S L S I V 11 4348 237 K T K Q I R R A V 114349 9 S A T D L G L S I 10 4350 12 D L G L S I S T L 10 4351 26 I F W FN V R E I 10 4352 31 V R E I S F N A C 10 4353 43 M F F I K F F T V 104354 52 M E S S V L L A M 10 4355 54 S S V L L A M A F 10 4356 68 V S NP L R Y A M 10 4357 78 L T D S R I A Q I 10 4358 83 I A Q I G V A S V 104359 98 L T P M V A L L I 10 4360 132 T D T R I N S A V 10 4361 148 T VG V D L L L I 10 4362 153 L L L I L L S Y V 10 4363 159 S Y V L I I R TV 10 4364 175 E R K E T F S T C 10 4365 187 I V A F A I Y Y I 10 4366190 F A I Y Y I P L I 10 4367 194 Y I P L I S L S I 10 4368 215 H T M IA N T Y L 10 4369 225 I S P L M N P V I 10 4370 228 L M N P V I Y S V 104371 233 I Y S V K T K Q I 10 4372 19 T L V T M L S I F 9 4373 23 M L SI F W F N V 9 4374 44 F F I K F F T V M 9 4375 48 F F T V M E S S V 94376 57 L L A M A F D R F 9 4377 138 S A V G L T A M F 9 4378 143 T A MF S T V G V 9 4379 179 T F S T C V S H I 9 4380 180 F S T C V S H I V 94381 184 V S H I V A F A I 9 4382 209 Q A P A Y V H T M 9 4383 210 A P AY V H T M I 9 4384 217 M I A N T Y L L I 9 4385 224 L I S P L M N P V 94386 240 Q I R R A V I K I 9 4387 21 V T M L S I F W F 8 4388 28 W F N VR E I S F 8 4389 35 S F N A C L S H M 8 4390 36 F N A C L S H M F 8 439137 N A C L S H M F F 8 4392 40 L S H M F F I K F 8 4393 41 S H M F F I KF F 8 4394 58 L A M A F D R F V 8 4395 69 S N P L R Y A M I 8 4396 80 DS R I A Q I G V 8 4397 119 S Y C Y H P D V M 8 4398 137 N S A V G L T AM 8 4399 172 S P E E R K E T F 8 4400 206 F G K Q A P A Y V 8 4401 238 TK Q I R R A V I 8 4402 82 R I A Q I G V A S 6 4403 135 R I N S A V G L T6 4404 165 R T V L S V A S P 6 4405 205 R F G K Q A P A Y 6 4406 243 R AV I K I L H S 6 4407 73 R Y A M I L T D S 5 4408 144 A M F S T V G V D 54409 191 A I Y Y I P L I S 5 4410 207 G K Q A P A Y V H 5 4411 239 K Q IR R A V I K 5 4412 14 G L S I S T L V T 4 4413 22 T M L S I F W F N 44414 25 S I F W F N V R E 4 4415 34 I S F N A C L S H 4 4416 46 I K F FT V M E S 4 4417 47 K F F T V M E S S 4 4418 66 V A V S N P L R Y 4 441986 I G V A S V I R G 4 4420 102 V A L L I R L S Y 4 4421 152 D L L L I LL S Y 4 4422 166 T V L S V A S P E 4 4423 178 E T F S T C V S H 4 4424188 V A F A I Y Y I P 4 4425 208 K Q A P A Y V H T 4 4426 2 Y Y F L S ML S A 3 4427 3 Y F L S M L S A T 3 4428 6 S M L S A T D L G 3 4429 42 HM F F I K F F T 3 4430 51 V M E S S V L L A 3 4431 56 V L L A M A F D R3 4432 76 M I L T D S R I A 3 4433 103 A L L I R L S Y C 3 4434 110 Y CH S Q V L H H 3 4435 114 Q V L H H S Y C Y 3 4436 120 Y C Y H P D V M K3 4437 127 M K L S C T D T R 3 4438 151 V D L L L I L L S 3 4439 158 L SY V L I I R T 3 4440 177 K E T F S T C V S 3 4441 214 V H T M I A N T Y3 4442 222 Y L L I S P L M N 3 4443 223 L L I S P L M N P 3 4444 226 S PL M N P V I Y 3 4445 232 V I Y S V K T K Q 3 4446 244 A V I K I L H S K3 4447 1 M Y Y F L S M L S 2 4448 11 T D L G L S I S T 2 4449 17 I S T LV T M L S 2 4450 27 F W F N V R E I S 2 4451 30 N V R E I S F N A 2 445255 S V L L A M A F D 2 4453 59 A M A F D R F V A 2 4454 61 A F D R F V AV S 2 4455 62 F D R F V A V S N 2 4456 77 I L T D S R I A Q 2 4457 79 TD S R I A Q I G 2 4458 104 L L I R L S Y C H 2 4459 116 L H H S Y C Y HP 2 4460 130 S C T D T R I N S 2 4461 136 I N S A V G L T A 2 4462 139 AV G L T A M F S 2 4463 140 V G L T A M F S T 2 4464 161 V L I I R T V LS 2 4465 169 S V A S P E E R K 2 4466 183 C V S H I V A F A 2 4467 186 HI V A F A I Y Y 2 4468 193 Y Y I P L I S L S 2 4469 196 P L I S L S I VH 2 4470 202 I V H R F G K Q A 2 4471 211 P A Y V H T M I A 2 4472 212 AY V H T M I A N 2 4473 218 I A N T Y L L I S 2 4474 219 A N T Y L L I SP 2 4475 230 N P V I Y S V K T 2 4476 231 P V I Y S V K T K 2 4477 236 VK T K Q I R R A 2 4478 246 I K I L H S K E T 2 4479 8 L S A T D L G L S1 4480 10 A T D L G L S I S 1 4481 20 L V T M L S I F W 1 4482 24 L S IF W F N V R 1 4483 29 F N V R E I S F N 1 4484 33 E I S F N A C L S 14485 45 F I K F F T V M E 1 4486 65 F V A V S N P L R 1 4487 67 A V S NP L R Y A 1 4488 85 Q I G V A S V I R 1 4489 99 T P M V A L L I R 1 4490109 S Y C H S Q V L H 1 4491 113 S Q V L H H S Y C 1 4492 123 H P D V MK L S C 1 4493 124 P D V M K L S C T 1 4494 129 L S C T D T R I N 1 4495163 I I R T V L S V A 1 4496 167 V L S V A S P E E 1 4497 168 L S V A SP E E R 1 4498 170 V A S P E E R K E 1 4499 171 A S P E E R K E T 1 4500185 S H I V A F A I Y 1 4501 197 L I S L S I V H R 1 4502 200 L S I V HR F G K 1 4503 201 S I V H R F G K Q 1 4504 213 Y V H T M I A N T 1 4505227 P L M N P V I Y S 1 4506 229 M N P V I Y S V K 1 4507 234 Y S V K TK Q I R 1 4508 235 S V K T K Q I R R 1 4509 HLA-B*4402 9-mers v.1:238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 32 R E I S F N A C L 23 451041 S H M F F I K F F 17 4511 84 A Q I G V A S V I 17 4512 90 S V I R G LL M L 17 4513 134 T R I N S A V G L 16 4514 182 T C V S H I V A F 164515 216 T M I A N T Y L L 16 4516 12 D L G L S I S T L 15 4517 21 V T ML S I F W F 15 4518 52 M E S S V L L A M 15 4519 54 S S V L L A M A F 154520 75 A M I L T D S R I 15 4521 96 L M L T P M V A L 15 4522 97 M L TP M V A L L 15 4523 102 V A L L I R L S Y 15 4524 121 C Y H P D V M K L15 4525 150 G V D L L L I L L 15 4526 152 D L L L I L L S Y 15 4527 154L L I L L S Y V L 15 4528 185 S H I V A F A I Y 15 4529 190 F A I Y Y IP L I 15 4530 220 N T Y L L I S P L 15 4531 226 S P L M N P V I Y 154532 241 I R R A V I K I L 15 4533 16 S I S T L V T M L 14 4534 70 N P LR Y A M I L 14 4535 78 L T D S R I A Q I 14 4536 87 G V A S V I R G L 144537 88 V A S V I R G L L 14 4538 147 S T V G V D L L L 14 4539 160 Y VL I I R T V L 14 4540 189 A F A I Y Y I P L 14 4541 198 I S L S I V H RF 14 4542 214 V H T M I A N T Y 14 4543 5 L S M L S A T D L 13 4544 40 LS H M F F I K F 13 4545 50 T V M E S S V L L 13 4546 66 V A V S N P L RY 13 4547 138 S A V G L T A M F 13 4548 145 M F S T V G V D L 13 4549149 V G V D L L L I L 13 4550 172 S P E E R K E T F 13 4551 174 E E R KE T F S T 13 4552 177 K E T F S T C V S 13 4553 205 R F G K Q A P A Y 134554 233 I Y S V K T K Q I 13 4555 7 M L S A T D L G L 12 4556 19 T L VT M L S I F 12 4557 28 W F N V R E I S F 12 4558 37 N A C L S H M F F 124559 38 A C L S H M F F I 12 4560 69 S N P L R Y A M I 12 4561 98 L T PM V A L L I 12 4562 100 P M V A L L I R L 12 4563 146 F S T V G V D L L12 4564 155 L I L L S Y V L I 12 4565 186 H I V A F A I Y Y 12 4566 192I Y Y I P L I S L 12 4567 194 Y I P L I S L S I 12 4568 240 Q I R R A VI K I 12 4569 9 S A T D L G L S I 11 4570 18 S T L V T M L S I 11 457120 L V T M L S I F W 11 4572 26 I F W F N V R E I 11 4573 36 F N A C L SH M F 11 4574 49 F T V M E S S V L 11 4575 57 L L A M A F D R F 11 457664 R F V A V S N P L 11 4577 108 L S Y C H S Q V L 11 4578 112 H S Q V LH H S Y 11 4579 114 Q V L H H S Y C Y 11 4580 148 T V G V D L L L I 114581 156 I L L S Y V L I I 11 4582 173 P E E R K E T F S 11 4583 179 T FS T C V S H I 11 4584 184 V S H I V A F A I 11 4585 187 I V A F A I Y YI 11 4586 210 A P A Y V H T M I 11 4587 215 H T M I A N T Y L 11 4588217 M I A N T Y L L I 11 4589 225 I S P L M N P V I 11 4590 238 T K Q IR R A V I 11 4591 128 K L S C T D T R I 10 4592 193 Y Y I P L I S L S 104593 244 A V I K I L H S K 9 4594 60 M A F D R F V A V 8 4595 81 S R I AQ I G V A 8 4596 159 S Y V L I I R T V 8 4597 239 K Q I R R A V I K 84598 61 A F D R F V A V S 7 4599 67 A V S N P L R Y A 7 4600 131 C T D TR I N S A 7 4601 144 A M F S T V G V D 7 4602 151 V D L L L I L L S 74603 161 V L I I R T V L S 7 4604 171 A S P E E R K E T 7 4605 231 P V IY S V K T K 7 4606 10 A T D L G L S I S 6 4607 15 L S I S T L V T M 64608 24 L S I F W F N V R 6 4609 33 E I S F N A C L S 6 4610 68 V S N PL R Y A M 6 4611 89 A S V I R G L L M 6 4612 101 M V A L L I R L S 64613 103 A L L I R L S Y C 6 4614 162 L I I R T V L S V 6 4615 170 V A SP E E R K E 6 4616 191 A I Y Y I P L I S 6 4617 197 L I S L S I V H R 64618 212 A Y V H T M I A N 6 4619 228 L M N P V I Y S V 6 4620 237 K T KQ I R R A V 6 4621 246 I K I L H S K E T 6 4622 44 F F I K F F T V M 54623 59 A M A F D R F V A 5 4624 72 L R Y A M I L T D 5 4625 77 I L T DS R I A Q 5 4626 122 Y H P D V M K L S 5 4627 139 A V G L T A M F S 54628 178 E T F S T C V S H 5 4629 196 P L I S L S I V H 5 4630 208 K Q AP A Y V H T 5 4631 219 A N T Y L L I S P 5 4632 224 L I S P L M N P V 54633 2 Y Y F L S M L S A 4 4634 3 Y F L S M L S A T 4 4635 6 S M L S A TD L G 4 4636 14 G L S I S T L V T 4 4637 25 S I F W F N V R E 4 4638 27F W F N V R E I S 4 4639 29 F N V R E I S F N 4 4640 31 V R E I S F N AC 4 4641 34 I S F N A C L S H 4 4642 43 M F F I K F F T V 4 4643 47 K FF T V M E S S 4 4644 53 E S S V L L A M A 4 4645 79 T D S R I A Q I G 44646 82 R I A Q I G V A S 4 4647 95 L L M L T P M V A 4 4648 104 L L I RL S Y C H 4 4649 130 S C T D T R I N S 4 4650 132 T D T R I N S A V 44651 137 N S A V G L T A M 4 4652 158 L S Y V L I I R T 4 4653 175 E R KE T F S T C 4 4654 200 L S I V H R F G K 4 4655 201 S I V H R F G K Q 44656 202 I V H R F G K Q A 4 4657 209 Q A P A Y V H T M 4 4658 213 Y V HT M I A N T 4 4659 221 T Y L L I S P L M 4 4660 223 L L I S P L M N P 44661 227 P L M N P V I Y S 4 4662 236 V K T K Q I R R A 4 4663 243 R A VI K I L H S 4 4664 8 L S A T D L G L S 3 4665 11 T D L G L S I S T 34666 13 L G L S I S T L V 3 4667 17 I S T L V T M L S 3 4668 22 T M L SI F W F N 3 4669 42 H M F F I K F F T 3 4670 46 I K F F T V M E S 3 467151 V M E S S V L L A 3 4672 55 S V L L A M A F D 3 4673 63 D R F V A V SN P 3 4674 76 M I L T D S R I A 3 4675 91 V I R G L L M L T 3 4676 92 IR G L L M L T P 3 4677 93 R G L L M L T P M 3 4678 99 T P M V A L L I R3 4679 109 S Y C H S Q V L H 3 4680 111 C H S Q V L H H S 3 4681 119 S YC Y H P D V M 3 4682 127 M K L S C T D T R 3 4683 129 L S C T D T R I N3 4684 136 I N S A V G L T A 3 4685 143 T A M F S T V G V 3 4686 157 L LS Y V L I I R 3 4687 163 I I R T V L S V A 3 4688 164 I R T V L S V A S3 4689 181 S T C V S H I V A 3 4690 183 C V S H I V A F A 3 4691 188 V AF A I Y Y I P 3 4692 199 S L S I V H R F G 3 4693 204 H R F G K Q A P A3 4694 218 I A N T Y L L I S 3 4695 222 Y L L I S P L M N 3 4696 229 M NP V I Y S V K 3 4697 230 N P V I Y S V K T 3 4698 235 S V K T K Q I R R3 4699 242 R R A V I K I L H 3 4700 4 F L S M L S A T D 2 4701 30 N V RE I S F N A 2 4702 35 S F N A C L S H M 2 4703 39 C L S H M F F I K 24704 45 F I K F F T V M E 2 4705 56 V L L A M A F D R 2 4706 58 L A M AF D R F V 2 4707 62 F D R F V A V S N 2 4708 71 P L R Y A M I L T 2 470973 R Y A M I L T D S 2 4710 74 Y A M I L T D S R 2 4711 86 I G V A S V IR G 2 4712 94 G L L M L T P M V 2 4713 106 I R L S Y C H S Q 2 4714 107R L S Y C H S Q V 2 4715 110 Y C H S Q V L H H 2 4716 113 S Q V L H H SY C 2 4717 117 H H S Y C Y H P D 2 4718 123 H P D V M K L S C 2 4719 125D V M K L S C T D 2 4720 133 D T R I N S A V G 2 4721 135 R I N S A V GL T 2 4722 140 V G L T A M F S T 2 4723 141 G L T A M F S T V 2 4724 153L L L I L L S Y V 2 4725 165 R T V L S V A S P 2 4726 166 T V L S V A SP E 2 4727 195 I P L I S L S I V 2 4728 203 V H R F G K Q A P 2 4729 207G K Q A P A Y V H 2 4730 1 M Y Y F L S M L S 1 4731 23 M L S I F W F N V1 4732 65 F V A V S N P L R 1 4733 80 D S R I A Q I G V 1 4734 83 I A QI G V A S V 1 4735 85 Q I G V A S V I R 1 4736 105 L I R L S Y C H S 14737 120 Y C Y H P D V M K 1 4738 124 P D V M K L S C T 1 4739 126 V M KL S C T D T 1 4740 142 L T A M F S T V G 1 4741 167 V L S V A S P E E 14742 168 L S V A S P E E R 1 4743 169 S V A S P E E R K 1 4744 176 R K ET F S T C V 1 4745 180 F S T C V S H I V 1 4746 206 F G K Q A P A Y V 14747 211 P A Y V H T M I A 1 4748 232 V I Y S V K T K Q 1 4749 245 V I KI L H S K E 1 4750 HLA-B*5101 9-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9score SEQ ID 195 I P L I S L S I V 24 4751 60 M A F D R F V A V 23 4752190 F A I Y Y I P L I 23 4753 210 A P A Y V H T M I 23 4754 9 S A T D LG L S I 22 4755 58 L A M A F D R F V 22 4756 83 I A Q I G V A S V 224757 70 N P L R Y A M I L 21 4758 143 T A M F S T V G V 21 4759 13 L G LS I S T L V 19 4760 156 I L L S Y V L I I 18 4761 225 I S P L M N P V I18 4762 84 A Q I G V A S V I 17 4763 88 V A S V I R G L L 17 4764 98 L TP M V A L L I 17 4765 209 Q A P A Y V H T M 17 4766 26 I F W F N V R E I16 4767 149 V G V D L L L I L 16 4768 155 L I L L S Y V L I 16 4769 206F G K Q A P A Y V 16 4770 218 I A N T Y L L I S 16 4771 108 L S Y C H SQ V L 15 4772 179 T F S T C V S H I 15 4773 230 N P V I Y S V K T 154774 240 Q I R R A V I K I 15 4775 12 D L G L S I S T L 14 4776 18 S T LV T M L S I 14 4777 43 M F F I K F F T V 14 4778 66 V A V S N P L R Y 144779 86 I G V A S V I R G 14 4780 102 V A L L I R L S Y 14 4781 160 Y VL I I R T V L 14 4782 162 L I I R T V L S V 14 4783 170 V A S P E E R KE 14 4784 172 S P E E R K E T F 14 4785 184 V S H I V A F A I 14 4786192 I Y Y I P L I S L 14 4787 194 Y I P L I S L S I 14 4788 211 P A Y VH T M I A 14 4789 226 S P L M N P V I Y 14 4790 233 I Y S V K T K Q I 144791 238 T K Q I R R A V I 14 4792 243 R A V I K I L H S 14 4793 78 L TD S R I A Q I 13 4794 80 D S R I A Q I G V 13 4795 99 T P M V A L L I R13 4796 118 H S Y C Y H P D V 13 4797 128 K L S C T D T R I 13 4798 141G L T A M F S T V 13 4799 148 T V G V D L L L I 13 4800 153 L L L I L LS Y V 13 4801 187 I V A F A I Y Y I 13 4802 188 V A F A I Y Y I P 134803 217 M I A N T Y L L I 13 4804 228 L M N P V I Y S V 13 4805 241 I RR A V I K I L 13 4806 37 N A C L S H M F F 12 4807 38 A C L S H M F F I12 4808 72 L R Y A M I L T D 12 4809 74 Y A M I L T D S R 12 4810 75 A MI L T D S R I 12 4811 96 L M L T P M V A L 12 4812 123 H P D V M K L S C12 4813 159 S Y V L I I R T V 12 4814 220 N T Y L L I S P L 12 4815 5 LS M L S A T D L 11 4816 50 T V M E S S V L L 11 4817 69 S N P L R Y A MI 11 4818 93 R G L L M L T P M 11 4819 138 S A V G L T A M F 11 4820 145M F S T V G V D L 11 4821 154 L L I L L S Y V L 11 4822 180 F S T C V SH I V 11 4823 224 L I S P L M N P V 11 4824 7 M L S A T D L G L 10 482516 S I S T L V T M L 10 4826 48 F F T V M E S S V 10 4827 49 F T V M E SS V L 10 4828 64 R F V A V S N P L 10 4829 87 G V A S V I R G L 10 483094 G L L M L T P M V 10 4831 97 M L T P M V A L L 10 4832 100 P M V A LL I R L 10 4833 121 C Y H P D V M K L 10 4834 132 T D T R I N S A V 104835 134 T R I N S A V G L 10 4836 140 V G L T A M F S T 10 4837 147 S TV G V D L L L 10 4838 176 R K E T F S T C V 10 4839 232 V I Y S V K T KQ 10 4840 23 M L S I F W F N V 9 4841 146 F S T V G V D L L 9 4842 158 LS Y V L I I R T 9 4843 163 I I R T V L S V A 9 4844 237 K T K Q I R R AV 9 4845 90 S V I R G L L M L 8 4846 107 R L S Y C H S Q V 8 4847 136 IN S A V G L T A 8 4848 150 G V D L L L I L L 8 4849 152 D L L L I L L SY 8 4850 189 A F A I Y Y I P L 8 4851 215 H T M I A N T Y L 8 4852 216 TM I A N T Y L L 8 4853 15 L S I S T L V T M 7 4854 24 L S I F W F N V R7 4855 32 R E I S F N A C L 7 4856 44 F F I K F F T V M 7 4857 63 D R FV A V S N P 7 4858 95 L L M L T P M V A 7 4859 120 Y C Y H P D V M K 74860 122 Y H P D V M K L S 7 4861 125 D V M K L S C T D 7 4862 133 D T RI N S A V G 7 4863 144 A M F S T V G V D 7 4864 198 I S L S I V H R F 74865 222 Y L L I S P L M N 7 4866 3 Y F L S M L S A T 6 4867 40 L S H MF F I K F 6 4868 46 I K F F T V M E S 6 4869 56 V L L A M A F D R 6 4870110 Y C H S Q V L H H 6 4871 142 L T A M F S T V G 6 4872 157 L L S Y VL I I R 6 4873 166 T V L S V A S P E 6 4874 175 E R K E T F S T C 6 4875191 A I Y Y I P L I S 6 4876 197 L I S L S I V H R 6 4877 231 P V I Y SV K T K 6 4878 1 M Y Y F L S M L S 5 4879 2 Y Y F L S M L S A 5 4880 11T D L G L S I S T 5 4881 14 G L S I S T L V T 5 4882 51 V M E S S V L LA 5 4883 52 M E S S V L L A M 5 4884 61 A F D R F V A V S 5 4885 62 F DR F V A V S N 5 4886 76 M I L T D S R I A 5 4887 77 I L T D S R I A Q 54888 81 S R I A Q I G V A 5 4889 92 I R G L L M L T P 5 4890 106 I R L SY C H S Q 5 4891 127 M K L S C T D T R 5 4892 151 V D L L L I L L S 54893 168 L S V A S P E E R 5 4894 181 S T C V S H I V A 5 4895 207 G K QA P A Y V H 5 4896 213 Y V H T M I A N T 5 4897 214 V H T M I A N T Y 54898 229 M N P V I Y S V K 5 4899 236 V K T K Q I R R A 5 4900 8 L S A TD L G L S 4 4901 17 I S T L V T M L S 4 4902 19 T L V T M L S I F 4 490322 T M L S I F W F N 4 4904 25 S I F W F N V R E 4 4905 27 F W F N V R EI S 4 4906 31 V R E I S F N A C 4 4907 34 I S F N A C L S H 4 4908 47 KF F T V M E S S 4 4909 57 L L A M A F D R F 4 4910 105 L I R L S Y C H S4 4911 111 C H S Q V L H H S 4 4912 116 L H H S Y C Y H P 4 4913 119 S YC Y H P D V M 4 4914 129 L S C T D T R I N 4 4915 171 A S P E E R K E T4 4916 177 K E T F S T C V S 4 4917 196 P L I S L S I V H 4 4918 234 Y SV K T K Q I R 4 4919 235 S V K T K Q I R R 4 4920 4 F L S M L S A T D 34921 20 L V T M L S I F W 3 4922 21 V T M L S I F W F 3 4923 30 N V R EI S F N A 3 4924 35 S F N A C L S H M 3 4925 59 A M A F D R F V A 3 492665 F V A V S N P L R 3 4927 91 V I R G L L M L T 3 4928 101 M V A L L IR L S 3 4929 103 A L L I R L S Y C 3 4930 126 V M K L S C T D T 3 4931130 S C T D T R I N S 3 4932 131 C T D T R I N S A 3 4933 137 N S A V GL T A M 3 4934 164 I R T V L S V A S 3 4935 165 R T V L S V A S P 3 4936178 E T F S T C V S H 3 4937 182 T C V S H I V A F 3 4938 186 H I V A FA I Y Y 3 4939 193 Y Y I P L I S L S 3 4940 199 S L S I V H R F G 3 4941201 S I V H R F G K Q 3 4942 202 I V H R F G K Q A 3 4943 204 H R F G KQ A P A 3 4944 221 T Y L L I S P L M 3 4945 223 L L I S P L M N P 3 4946227 P L M N P V I Y S 3 4947 245 V I K I L H S K E 3 4948 246 I K I L HS K E T 3 4949 6 S M L S A T D L G 2 4950 29 F N V R E I S F N 2 4951 39C L S H M F F I K 2 4952 41 S H M F F I K F F 2 4953 45 F I K F F T V ME 2 4954 55 S V L L A M A F D 2 4955 67 A V S N P L R Y A 2 4956 73 R YA M I L T D S 2 4957 79 T D S R I A Q I G 2 4958 104 L L I R L S Y C H 24959 109 S Y C H S Q V L H 2 4960 114 Q V L H H S Y C Y 2 4961 115 V L HH S Y C Y H 2 4962 124 P D V M K L S C T 2 4963 135 R I N S A V G L T 24964 139 A V G L T A M F S 2 4965 161 V L I I R T V L S 2 4966 173 P E ER K E T F S 2 4967 183 C V S H I V A F A 2 4968 200 L S I V H R F G K 24969 205 R F G K Q A P A Y 2 4970 208 K Q A P A Y V H T 2 4971 212 A Y VH T M I A N 2 4972 219 A N T Y L L I S P 2 4973 239 K Q I R R A V I K 24974 244 A V I K I L H S K 2 4975 10 A T D L G L S I S 1 4976 28 W F N VR E I S F 1 4977 33 E I S F N A C L S 1 4978 36 F N A C L S H M F 1 497942 H M F F I K F F T 1 4980 53 E S S V L L A M A 1 4981 54 S S V L L A MA F 1 4982 68 V S N P L R Y A M 1 4983 71 P L R Y A M I L T 1 4984 part2 HLA-A*0201 9-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 16F L L T G V P G L 31 4985 13 S I I F L L T G V 27 4986 42 A L L G N S LI L 27 4987 32 S I P F C F L S V 22 4988 40 V T A L L G N S L 21 4989 1F I T S T L Q N I 20 4990 9 I T S T S I I F L 20 4991 62 P M Y Y F L S ML 20 4992 23 G L E A F H T W I 19 4993 30 W I S I P F C F L 19 4994 47 SL I L F A T I T 19 4995 4 S T L Q N I T S T 18 4996 35 F C F L S V T A L17 4997 49 I L F A T I T Q P 17 4998 51 F A T I T Q P S L 17 4999 36 C FL S V T A L L 16 5000 41 T A L L G N S L I 16 5001 43 L L G N S L I L F16 5002 58 S L H E P M Y Y F 16 5003 46 N S L I L F A T I 15 5004 48 L IL F A T I T Q 15 5005 54 I T Q P S L H E P 15 5006 5 T L Q N I T S T S14 5007 14 I I F L L T G V P 14 5008 18 L T G V P G L E A 14 5009 59 L HE P M Y Y F L 14 5010 6 L Q N I T S T S I 13 5011 10 T S T S I I F L L13 5012 17 L L T G V P G L E 13 5013 44 L G N S L I L F A 13 5014 2 I TS T L Q N I T 12 5015 7 Q N I T S T S I I 12 5016 25 E A F H T W I S I12 5017 33 I P F C F L S V T 12 5018 37 F L S V T A L L G 12 5019 11 S TS I I F L L T 11 5020 12 T S I I F L L T G 10 5021 20 G V P G L E A F H10 5022 28 H T W I S I P F C 10 5023 39 S V T A L L G N S 10 5024 45 G NS L I L F A T 10 5025 19 T G V P G L E A F 9 5026 53 T I T Q P S L H E 95027 38 L S V T A L L G N 8 5028 52 A T I T Q P S L H 8 5029 8 N I T S TS I I F 7 5030 31 I S I P F C F L S 7 5031 15 I F L L T G V P G 6 503226 A F H T W I S I P 6 5033 50 L F A T I T Q P S 6 5034 21 V P G L E A FH T 5 5035 24 L E A F H T W I S 5 5036 34 P F C F L S V T A 5 5037 55 TQ P S L H E P M 5 5038 61 E P M Y Y F L S M 5 5039 22 P G L E A F H T W4 5040 29 T W I S I P F C F 2 5041 3 T S T L Q N I T S 1 5042 56 Q P S LH E P M Y 1 5043 60 H E P M Y Y F L S 1 5044 57 P S L H E P M Y Y −15045 HLA-A1 9-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 11 ST S I I F L L T 19 5046 57 P S L H E P M Y Y 19 5047 56 Q P S L H E P MY 16 5048 18 L T G V P G L E A 14 5049 59 L H E P M Y Y F L 14 5050 3 TS T L Q N I T S 11 5051 23 G L E A F H T W I 11 5052 32 S I P F C F L SV 11 5053 52 A T I T Q P S L H 11 5054 9 I T S T S I I F L 10 5055 12 TS I I F L L T G 10 5056 31 I S I P F C F L S 10 5057 37 F L S V T A L LG 10 5058 38 L S V T A L L G N 10 5059 54 I T Q P S L H E P 10 5060 61 EP M Y Y F L S M 10 5061 42 A L L G N S L I L 9 5062 4 S T L Q N I T S T8 5063 40 V T A L L G N S L 8 5064 43 L L G N S L I L F 7 5065 46 N S LI L F A T I 7 5066 53 T I T Q P S L H E 7 5067 2 I T S T L Q N I T 65068 10 T S T S I I F L L 6 5069 17 L L T G V P G L E 6 5070 19 T G V PG L E A F 6 5071 28 H T W I S I P F C 6 5072 44 L G N S L I L F A 6 507316 F L L T G V P G L 5 5074 27 F H T W I S I P F 5 5075 41 T A L L G N SL I 5 5076 8 N I T S T S I I F 4 5077 25 E A F H T W I S I 4 5078 30 W IS I P F C F L 4 5079 36 C F L S V T A L L 4 5080 48 L I L F A T I T Q 45081 58 S L H E P M Y Y F 4 5082 22 P G L E A F H T W 3 5083 47 S L I LF A T I T 3 5084 60 H E P M Y Y F L S 3 5085 13 S I I F L L T G V 2 508635 F C F L S V T A L 2 5087 39 S V T A L L G N S 2 5088 1 F I T S T L QN I 1 5089 5 T L Q N I T S T S 1 5090 14 I I F L L T G V P 1 5091 15 I FL L T G V P G 1 5092 20 G V P G L E A F H 1 5093 21 V P G L E A F H T 15094 26 A F H T W I S I P 1 5095 33 I P F C F L S V T 1 5096 49 I L F AT I T Q P 1 5097 51 F A T I T Q P S L 1 5098 62 P M Y Y F L S M L 1 5099HLA-A26 9-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 58 S L HE P M Y Y F 24 5100 9 I T S T S I I F L 23 5101 43 L L G N S L I L F 235102 16 F L L T G V P G L 22 5103 30 W I S I P F C F L 22 5104 8 N I T ST S I I F 21 5105 40 V T A L L G N S L 21 5106 61 E P M Y Y F L S M 195107 13 S I I F L L T G V 18 5108 42 A L L G N S L I L 18 5109 54 I T QP S L H E P 18 5110 1 F I T S T L Q N I 17 5111 19 T G V P G L E A F 175112 4 S T L Q N I T S T 16 5113 28 H T W I S I P F C 16 5114 32 S I P FC F L S V 16 5115 35 F C F L S V T A L 16 5116 36 C F L S V T A L L 165117 39 S V T A L L G N S 16 5118 20 G V P G L E A F H 15 5119 49 I L FA T I T Q P 15 5120 11 S T S I I F L L T 14 5121 52 A T I T Q P S L H 145122 59 L H E P M Y Y F L 14 5123 62 P M Y Y F L S M L 14 5124 10 T S TS I I F L L 13 5125 14 I I F L L T G V P 13 5126 29 T W I S I P F C F 135127 53 T I T Q P S L H E 12 5128 56 Q P S L H E P M Y 12 5129 2 I T S TL Q N I T 11 5130 18 L T G V P G L E A 11 5131 26 A F H T W I S I P 115132 55 T Q P S L H E P M 11 5133 57 P S L H E P M Y Y 11 5134 17 L L TG V P G L E 10 5135 27 F H T W I S I P F 10 5136 47 S L I L F A T I T 105137 48 L I L F A T I T Q 10 5138 51 F A T I T Q P S L 10 5139 5 T L Q NI T S T S 9 5140 25 E A F H T W I S I 9 5141 23 G L E A F H T W I 8 514234 P F C F L S V T A 8 5143 37 F L S V T A L L G 8 5144 50 L F A T I T QP S 8 5145 15 I F L L T G V P G 7 5146 33 I P F C F L S V T 7 5147 12 TS I I F L L T G 6 5148 22 P G L E A F H T W 6 5149 44 L G N S L I L F A6 5150 46 N S L I L F A T I 6 5151 38 L S V T A L L G N 5 5152 45 G N SL I L F A T 5 5153 60 H E P M Y Y F L S 5 5154 7 Q N I T S T S I I 45155 31 I S I P F C F L S 4 5156 3 T S T L Q N I T S 1 5157 6 L Q N I TS T S I 1 5158 21 V P G L E A F H T 1 5159 24 L E A F H T W I S 1 516041 T A L L G N S L I 1 5161 HLA-A3 9-mers v.1B: 238P1B2 Pos 1 2 3 4 5 67 8 9 score SEQ ID 42 A L L G N S L I L 20 5162 20 G V P G L E A F H 195163 47 S L I L F A T I T 19 5164 5 T L Q N I T S T S 18 5165 49 I L F AT I T Q P 18 5166 14 I I F L L T G V P 16 5167 37 F L S V T A L L G 165168 58 S L H E P M Y Y F 16 5169 17 L L T G V P G L E 15 5170 43 L L GN S L I L F 15 5171 16 F L L T G V P G L 14 5172 23 G L E A F H T W I 145173 32 S I P F C F L S V 14 5174 39 S V T A L L G N S 14 5175 48 L I LF A T I T Q 14 5176 52 A T I T Q P S L H 14 5177 13 S I I F L L T G V 135178 8 N I T S T S I I F 12 5179 15 I F L L T G V P G 12 5180 12 T S I IF L L T G 11 5181 53 T I T Q P S L H E 11 5182 19 T G V P G L E A F 105183 46 N S L I L F A T I 10 5184 56 Q P S L H E P M Y 10 5185 57 P S LH E P M Y Y 10 5186 30 W I S I P F C F L 9 5187 33 I P F C F L S V T 95188 1 F I T S T L Q N I 8 5189 7 Q N I T S T S I I 8 5190 29 T W I S IP F C F 8 5191 31 I S I P F C F L S 8 5192 34 P F C F L S V T A 8 519341 T A L L G N S L I 8 5194 62 P M Y Y F L S M L 8 5195 22 P G L E A F HT W 7 5196 40 V T A L L G N S L 7 5197 4 S T L Q N I T S T 6 5198 18 L TG V P G L E A 6 5199 26 A F H T W I S I P 6 5200 36 C F L S V T A L L 65201 3 T S T L Q N I T S 5 5202 11 S T S I I F L L T 5 5203 54 I T Q P SL H E P 5 5204 61 E P M Y Y F L S M 5 5205 6 L Q N I T S T S I 4 5206 21V P G L E A F H T 4 5207 27 F H T W I S I P F 4 5208 35 F C F L S V T AL 3 5209 38 L S V T A L L G N 3 5210 44 L G N S L I L F A 3 5211 51 F AT I T Q P S L 3 5212 59 L H E P M Y Y F L 3 5213 2 I T S T L Q N I T 25214 9 I T S T S I I F L 2 5215 25 E A F H T W I S I 2 5216 45 G N S L IL F A T 2 5217 24 L E A F H T W I S 1 5218 28 H T W I S I P F C 1 521950 L F A T I T Q P S 1 5220 HLA-B*0702 9-mers v.1B: 238P1B2 Pos 1 2 3 45 6 7 8 9 score SEQ ID 61 E P M Y Y F L S M 21 5221 33 I P F C F L S V T18 5222 21 V P G L E A F H T 17 5223 30 W I S I P F C F L 17 5224 42 A LL G N S L I L 16 5225 9 I T S T S I I F L 14 5226 18 L T G V P G L E A13 5227 35 F C F L S V T A L 13 5228 56 Q P S L H E P M Y 13 5229 16 F LL T G V P G L 12 5230 36 C F L S V T A L L 12 5231 40 V T A L L G N S L12 5232 59 L H E P M Y Y F L 12 5233 11 S T S I I F L L T 11 5234 51 F AT I T Q P S L 11 5235 10 T S T S I I F L L 10 5236 62 P M Y Y F L S M L10 5237 2 I T S T L Q N I T 9 5238 32 S I P F C F L S V 9 5239 44 L G NS L I L F A 9 5240 45 G N S L I L F A T 9 5241 58 S L H E P M Y Y F 95242 19 T G V P G L E A F 8 5243 23 G L E A F H T W I 8 5244 34 P F C FL S V T A 8 5245 46 N S L I L F A T I 8 5246 4 S T L Q N I T S T 7 52476 L Q N I T S T S I 7 5248 7 Q N I T S T S I I 7 5249 13 S I I F L L T GV 7 5250 25 E A F H T W I S I 7 5251 27 F H T W I S I P F 7 5252 43 L LG N S L I L F 7 5253 47 S L I L F A T I T 7 5254 55 T Q P S L H E P M 75255 1 F I T S T L Q N I 6 5256 8 N I T S T S I I F 6 5257 29 T W I S IP F C F 6 5258 41 T A L L G N S L I 6 5259 15 I F L L T G V P G 5 526053 T I T Q P S L H E 5 5261 20 G V P G L E A F H 4 5262 37 F L S V T A LL G 4 5263 14 I I F L L T G V P 3 5264 49 I L F A T I T Q P 3 5265 50 LF A T I T Q P S 3 5266 12 T S I I F L L T G 2 5267 17 L L T G V P G L E2 5268 24 L E A F H T W I S 2 5269 26 A F H T W I S I P 2 5270 28 H T WI S I P F C 2 5271 31 I S I P F C F L S 2 5272 38 L S V T A L L G N 25273 52 A T I T Q P S L H 2 5274 54 I T Q P S L H E P 2 5275 5 T L Q N IT S T S 1 5276 22 P G L E A F H T W 1 5277 39 S V T A L L G N S 1 527848 L I L F A T I T Q 1 5279 HLA-B*08 9-mers v.1B: 238P1B2 Pos 1 2 3 4 56 7 8 9 score SEQ ID 16 F L L T G V P G L 18 5280 42 A L L G N S L I L16 5281 58 S L H E P M Y Y F 16 5282 51 F A T I T Q P S L 15 5283 30 W IS I P F C F L 14 5284 35 F C F L S V T A L 14 5285 23 G L E A F H T W I13 5286 9 I T S T S I I F L 12 5287 25 E A F H T W I S I 12 5288 40 V TA L L G N S L 12 5289 41 T A L L G N S L I 12 5290 43 L L G N S L I L F12 5291 1 F I T S T L Q N I 11 5292 10 T S T S I I F L L 11 5293 62 P MY Y F L S M L 11 5294 8 N I T S T S I I F 10 5295 36 C F L S V T A L L10 5296 59 L H E P M Y Y F L 10 5297 47 S L I L F A T I T 9 5298 61 E PM Y Y F L S M 9 5299 21 V P G L E A F H T 8 5300 37 F L S V T A L L G 85301 49 I L F A T I T Q P 8 5302 19 T G V P G L E A F 7 5303 27 F H T WI S I P F 7 5304 33 I P F C F L S V T 7 5305 56 Q P S L H E P M Y 7 53065 T L Q N I T S T S 6 5307 6 L Q N I T S T S I 6 5308 7 Q N I T S T S II 6 5309 13 S I I F L L T G V 6 5310 14 I I F L L T G V P 6 5311 17 L LT G V P G L E 6 5312 29 T W I S I P F C F 6 5313 32 S I P F C F L S V 65314 46 N S L I L F A T I 6 5315 48 L I L F A T I T Q 4 5316 53 T I T QP S L H E 4 5317 4 S T L Q N I T S T 3 5318 15 I F L L T G V P G 3 531945 G N S L I L F A T 3 5320 3 T S T L Q N I T S 2 5321 11 S T S I I F LL T 2 5322 18 L T G V P G L E A 2 5323 22 P G L E A F H T W 2 5324 28 HT W I S I P F C 2 5325 39 S V T A L L G N S 2 5326 54 I T Q P S L H E P2 5327 2 I T S T L Q N I T 1 5328 20 G V P G L E A F H 1 5329 26 A F H TW I S I P 1 5330 31 I S I P F C F L S 1 5331 34 P F C F L S V T A 1 533244 L G N S L I L F A 1 5333 60 H E P M Y Y F L S 1 5334 HLA-B*15109-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 59 L H E P M Y YF L 23 5335 27 F H T W I S I P F 16 5336 9 I T S T S I I F L 14 5337 16F L L T G V P G L 13 5338 10 T S T S I I F L L 12 5339 30 W I S I P F CF L 12 5340 35 F C F L S V T A L 12 5341 42 A L L G N S L I L 12 5342 19T G V P G L E A F 11 5343 40 V T A L L G N S L 11 5344 51 F A T I T Q PS L 11 5345 36 C F L S V T A L L 10 5346 62 P M Y Y F L S M L 10 5347 58S L H E P M Y Y F 9 5348 29 T W I S I P F C F 8 5349 55 T Q P S L H E PM 7 5350 61 E P M Y Y F L S M 7 5351 8 N I T S T S I I F 6 5352 43 L L GN S L I L F 6 5353 54 I T Q P S L H E P 5 5354 14 I I F L L T G V P 45355 15 I F L L T G V P G 4 5356 31 I S I P F C F L S 4 5357 33 I P F CF L S V T 4 5358 2 I T S T L Q N I T 3 5359 4 S T L Q N I T S T 3 536018 L T G V P G L E A 3 5361 34 P F C F L S V T A 3 5362 45 G N S L I L FA T 3 5363 49 I L F A T I T Q P 3 5364 53 T I T Q P S L H E 3 5365 3 T ST L Q N I T S 2 5366 5 T L Q N I T S T S 2 5367 12 T S I I F L L T G 25368 17 L L T G V P G L E 2 5369 20 G V P G L E A F H 2 5370 22 P G L EA F H T W 2 5371 23 G L E A F H T W I 2 5372 28 H T W I S I P F C 2 537337 F L S V T A L L G 2 5374 41 T A L L G N S L I 2 5375 56 Q P S L H E PM Y 2 5376 11 S T S I I F L L T 1 5377 24 L E A F H T W I S 1 5378 25 EA F H T W I S I 1 5379 26 A F H T W I S I P 1 5380 44 L G N S L I L F A1 5381 46 N S L I L F A T I 1 5382 48 L I L F A T I T Q 1 5383 50 L F AT I T Q P S 1 5384 52 A T I T Q P S L H 1 5385 57 P S L H E P M Y Y 15386 HLA-B*2705 9-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID35 F C F L S V T A L 18 5387 42 A L L G N S L I L 17 5388 9 I T S T S II F L 16 5389 16 F L L T G V P G L 16 5390 19 T G V P G L E A F 15 539120 G V P G L E A F H 15 5392 10 T S T S I I F L L 14 5393 36 C F L S V TA L L 14 5394 40 V T A L L G N S L 14 5395 51 F A T I T Q P S L 14 539662 P M Y Y F L S M L 14 5397 27 F H T W I S I P F 13 5398 29 T W I S I PF C F 13 5399 41 T A L L G N S L I 13 5400 43 L L G N S L I L F 13 540158 S L H E P M Y Y F 13 5402 8 N I T S T S I I F 12 5403 52 A T I T Q PS L H 12 5404 57 P S L H E P M Y Y 12 5405 59 L H E P M Y Y F L 12 540623 G L E A F H T W I 11 5407 25 E A F H T W I S I 11 5408 30 W I S I P FC F L 11 5409 46 N S L I L F A T I 11 5410 4 S T L Q N I T S T 10 5411 6L Q N I T S T S I 10 5412 7 Q N I T S T S I I 10 5413 49 I L F A T I T QP 10 5414 56 Q P S L H E P M Y 10 5415 61 E P M Y Y F L S M 10 5416 1 FI T S T L Q N I 9 5417 55 T Q P S L H E P M 9 5418 14 I I F L L T G V P7 5419 33 I P F C F L S V T 7 5420 13 S I I F L L T G V 6 5421 45 G N SL I L F A T 6 5422 47 S L I L F A T I T 6 5423 2 I T S T L Q N I T 55424 12 T S I I F L L T G 5 5425 15 I F L L T G V P G 5 5426 26 A F H TW I S I P 5 5427 28 H T W I S I P F C 5 5428 44 L G N S L I L F A 5 542953 T I T Q P S L H E 5 5430 54 I T Q P S L H E P 5 5431 3 T S T L Q N IT S 4 5432 22 P G L E A F H T W 4 5433 31 I S I P F C F L S 4 5434 34 PF C F L S V T A 4 5435 39 S V T A L L G N S 4 5436 48 L I L F A T I T Q4 5437 5 T L Q N I T S T S 3 5438 17 L L T G V P G L E 3 5439 18 L T G VP G L E A 3 5440 21 V P G L E A F H T 3 5441 38 L S V T A L L G N 3 544211 S T S I I F L L T 2 5443 32 S I P F C F L S V 2 5444 37 F L S V T A LL G 2 5445 24 L E A F H T W I S 1 5446 50 L F A T I T Q P S 1 5447HLA-B*2709 9-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 16 FL L T G V P G L 14 5448 42 A L L G N S L I L 14 5449 10 T S T S I I F LL 13 5450 35 F C F L S V T A L 13 5451 36 C F L S V T A L L 13 5452 51 FA T I T Q P S L 12 5453 59 L H E P M Y Y F L 12 5454 62 P M Y Y F L S ML 12 5455 1 F I T S T L Q N I 11 5456 9 I T S T S I I F L 11 5457 23 G LE A F H T W I 11 5458 29 T W I S I P F C F 11 5459 8 N I T S T S I I F10 5460 19 T G V P G L E A F 10 5461 25 E A F H T W I S I 10 5462 27 F HT W I S I P F 10 5463 30 W I S I P F C F L 10 5464 40 V T A L L G N S L10 5465 41 T A L L G N S L I 10 5466 46 N S L I L F A T I 10 5467 7 Q NI T S T S I I 9 5468 13 S I I F L L T G V 9 5469 32 S I P F C F L S V 95470 55 T Q P S L H E P M 9 5471 58 S L H E P M Y Y F 9 5472 61 E P M YY F L S M 9 5473 6 L Q N I T S T S I 8 5474 43 L L G N S L I L F 8 547515 I F L L T G V P G 4 5476 45 G N S L I L F A T 4 5477 49 I L F A T I TQ P 4 5478 14 I I F L L T G V P 3 5479 20 G V P G L E A F H 3 5480 31 IS I P F C F L S 3 5481 33 I P F C F L S V T 3 5482 4 S T L Q N I T S T 25483 11 S T S I I F L L T 2 5484 12 T S I I F L L T G 2 5485 22 P G L EA F H T W 2 5486 37 F L S V T A L L G 2 5487 38 L S V T A L L G N 2 548839 S V T A L L G N S 2 5489 44 L G N S L I L F A 2 5490 47 S L I L F A TI T 2 5491 48 L I L F A T I T Q 2 5492 52 A T I T Q P S L H 2 5493 53 TI T Q P S L H E 2 5494 54 I T Q P S L H E P 2 5495 57 P S L H E P M Y Y2 5496 2 I T S T L Q N I T 1 5497 3 T S T L Q N I T S 1 5498 5 T L Q N IT S T S 1 5499 17 L L T G V P G L E 1 5500 18 L T G V P G L E A 1 550121 V P G L E A F H T 1 5502 26 A F H T W I S I P 1 5503 28 H T W I S I PF C 1 5504 34 P F C F L S V T A 1 5505 50 L F A T I T Q P S 1 5506 56 QP S L H E P M Y 1 5507 HLA-B*4402 9-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 78 9 score SEQ ID 42 A L L G N S L I L 17 5508 9 I T S T S I I F L 165509 19 T G V P G L E A F 16 5510 35 F C F L S V T A L 16 5511 10 T S TS I I F L L 15 5512 29 T W I S I P F C F 15 5513 22 P G L E A F H T W 145514 43 L L G N S L I L F 14 5515 7 Q N I T S T S I I 13 5516 16 F L L TG V P G L 13 5517 25 E A F H T W I S I 13 5518 36 C F L S V T A L L 135519 59 L H E P M Y Y F L 13 5520 8 N I T S T S I I F 12 5521 27 F H T WI S I P F 12 5522 30 W I S I P F C F L 12 5523 40 V T A L L G N S L 125524 46 N S L I L F A T I 12 5525 56 Q P S L H E P M Y 12 5526 57 P S LH E P M Y Y 12 5527 60 H E P M Y Y F L S 12 5528 24 L E A F H T W I S 115529 41 T A L L G N S L I 11 5530 58 S L H E P M Y Y F 11 5531 62 P M YY F L S M L 11 5532 51 F A T I T Q P S L 10 5533 1 F I T S T L Q N I 95534 52 A T I T Q P S L H 9 5535 6 L Q N I T S T S I 8 5536 23 G L E A FH T W I 8 5537 26 A F H T W I S I P 7 5538 31 I S I P F C F L S 7 5539 4S T L Q N I T S T 6 5540 11 S T S I I F L L T 6 5541 12 T S I I F L L TG 6 5542 45 G N S L I L F A T 6 5543 47 S L I L F A T I T 6 5544 49 I LF A T I T Q P 6 5545 13 S I I F L L T G V 5 5546 14 I I F L L T G V P 55547 54 I T Q P S L H E P 5 5548 61 E P M Y Y F L S M 5 5549 5 T L Q N IT S T S 4 5550 32 S I P F C F L S V 4 5551 33 I P F C F L S V T 4 555237 F L S V T A L L G 4 5553 44 L G N S L I L F A 4 5554 48 L I L F A T IT Q 4 5555 2 I T S T L Q N I T 3 5556 3 T S T L Q N I T S 3 5557 15 I FL L T G V P G 3 5558 17 L L T G V P G L E 3 5559 28 H T W I S I P F C 35560 38 L S V T A L L G N 3 5561 50 L F A T I T Q P S 3 5562 20 G V P GL E A F H 2 5563 21 V P G L E A F H T 2 5564 34 P F C F L S V T A 2 556539 S V T A L L G N S 2 5566 18 L T G V P G L E A 1 5567 53 T I T Q P S LH E 1 5568 55 T Q P S L H E P M 1 5569 HLA-B*5101 9-mers v.1B: 238P1B2Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 41 T A L L G N S L I 24 5570 25 E A FH T W I S I 23 5571 51 F A T I T Q P S L 18 5572 33 I P F C F L S V T 175573 46 N S L I L F A T I 16 5574 6 L Q N I T S T S I 14 5575 1 F I T ST L Q N I 13 5576 21 V P G L E A F H T 13 5577 22 P G L E A F H T W 135578 61 E P M Y Y F L S M 13 5579 7 Q N I T S T S I I 12 5580 9 I T S TS I I F L 12 5581 16 F L L T G V P G L 12 5582 23 G L E A F H T W I 125583 35 F C F L S V T A L 12 5584 32 S I P F C F L S V 11 5585 62 P M YY F L S M L 11 5586 13 S I I F L L T G V 10 5587 36 C F L S V T A L L 105588 42 A L L G N S L I L 10 5589 44 L G N S L I L F A 10 5590 56 Q P SL H E P M Y 10 5591 59 L H E P M Y Y F L 9 5592 10 T S T S I I F L L 85593 19 T G V P G L E A F 8 5594 40 V T A L L G N S L 8 5595 30 W I S IP F C F L 7 5596 48 L I L F A T I T Q 7 5597 49 I L F A T I T Q P 7 559814 I I F L L T G V P 6 5599 15 I F L L T G V P G 6 5600 17 L L T G V P GL E 6 5601 3 T S T L Q N I T S 5 5602 12 T S I I F L L T G 5 5603 38 L SV T A L L G N 5 5604 43 L L G N S L I L F 5 5605 2 I T S T L Q N I T 45606 4 S T L Q N I T S T 4 5607 37 F L S V T A L L G 4 5608 54 I T Q P SL H E P 4 5609 5 T L Q N I T S T S 3 5610 8 N I T S T S I I F 3 5611 18L T G V P G L E A 3 5612 28 H T W I S I P F C 3 5613 34 P F C F L S V TA 3 5614 50 L F A T I T Q P S 3 5615 53 T I T Q P S L H E 3 5616 57 P SL H E P M Y Y 3 5617 11 S T S I I F L L T 2 5618 20 G V P G L E A F H 25619 24 L E A F H T W I S 5620 HLA-A*0201 9-mers v.2: 238P1B2 Pos 1 2 34 5 6 7 8 9 score SEQ ID 8 L T S P L M N P V 20 5621 4 N T Y L L T S P L18 5622 7 L L T S P L M N P 16 5623 1 M I A N T Y L L T 15 5624 2 I A NT Y L L T S 15 5625 6 Y L L T S P L M N 15 5626 9 T S P L M N P V I 95627 3 A N T Y L L T S P 7 5628 5 T Y L L T S P L M 7 5629 HLA-A1 9-mersv.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 6 Y L L T S P L M N 105630 8 L T S P L M N P V 10 5631 1 M I A N T Y L L T 8 5632 2 I A N T YL L T S 7 5633 4 N T Y L L T S P L 6 5634 9 T S P L M N P V I 6 5635 5 TY L L T S P L M 2 5636 7 L L T S P L M N P 2 5637 3 A N T Y L L T S P 15638 HLA-A26 9-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 4 NT Y L L T S P L 20 5639 8 L T S P L M N P V 17 5640 1 M I A N T Y L L T15 5641 7 L L T S P L M N P 15 5642 6 Y L L T S P L M N 10 5643 5 T Y LL T S P L M 9 5644 3 A N T Y L L T S P 6 5645 2 I A N T Y L L T S 4 56469 T S P L M N P V I 2 5647 HLA-A3 9-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 78 9 score SEQ ID 6 Y L L T S P L M N 17 5648 1 M I A N T Y L L T 13 56497 L L T S P L M N P 11 5650 2 I A N T Y L L T S 9 5651 4 N T Y L L T S PL 8 5652 3 A N T Y L L T S P 6 5653 9 T S P L M N P V I 5 5654 5 T Y L LT S P L M 3 5655 8 L T S P L M N P V 3 5656 HLA-B*0702 9-mers v.2:238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 4 N T Y L L T S P L 12 5657 8L T S P L M N P V 10 5658 1 M I A N T Y L L T 9 5659 9 T S P L M N P V I8 5660 5 T Y L L T S P L M 7 5661 2 I A N T Y L L T S 3 5662 3 A N T Y LL T S P 3 5663 7 L L T S P L M N P 3 5664 6 Y L L T S P L M N 2 5665HLA-B*08 9-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 4 N T YL L T S P L 11 5666 9 T S P L M N P V I 8 5667 6 Y L L T S P L M N 65668 7 L L T S P L M N P 6 5669 2 I A N T Y L L T S 5 5670 1 M I A N T YL L T 4 5671 3 A N T Y L L T S P 1 5672 5 T Y L L T S P L M 1 5673HLA-B*1510 9-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 4 N TY L L T S P L 10 5674 5 T Y L L T S P L M 8 5675 8 L T S P L M N P V 45676 9 T S P L M N P V I 4 5677 2 I A N T Y L L T S 3 5678 6 Y L L T S PL M N 2 5679 1 M I A N T Y L L T 1 5680 7 L L T S P L M N P 1 5681HLA-B*2705 9-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 4 N TY L L T S P L 15 5682 5 T Y L L T S P L M 13 5683 9 T S P L M N P V I 105684 3 A N T Y L L T S P 6 5685 7 L L T S P L M N P 5 5686 2 I A N T Y LL T S 4 5687 6 Y L L T S P L M N 4 5688 8 L T S P L M N P V 3 5689 1 M IA N T Y L L T 1 5690 HLA-B*2709 9-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 89 score SEQ ID 4 N T Y L L T S P L 12 5691 5 T Y L L T S P L M 11 5692 8L T S P L M N P V 9 5693 9 T S P L M N P V I 9 5694 6 Y L L T S P L M N3 5695 7 L L T S P L M N P 3 5696 2 I A N T Y L L T S 2 5697 3 A N T Y LL T S P 2 5698 1 M I A N T Y L L T 1 5699 HLA-B*4402 9-mers v.2: 238P1B2Pos 1 2 3 4 5 6 7 8 9 score SEQ ID 4 N T Y L L T S P L 13 5700 9 T S P LM N P V I 11 5701 8 L T S P L M N P V 5702

TABLE XIXB HLA-A*0201 10-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 scoreSEQ ID 161 V L I I R T V L S V 30 5703 82 R I A Q I G V A S V 28 5704 96L M L T P M V A L L 28 5705 77 I L T D S R I A Q I 26 5706 95 L L M L TP M V A L 26 5707 191 A I Y Y I P L I S L 26 5708 25 S I F W F N V R E I25 5709 152 D L L L I L L S Y V 25 5710 153 L L L I L L S Y V L 25 5711155 L I L L S Y V L I I 25 5712 223 L L I S P L M N P V 25 5713 227 P LM N P V I Y S V 25 5714 6 S M L S A T D L G L 24 5715 57 L L A M A F D RF V 24 5716 59 A M A F D R F V A V 24 5717 154 L L I L L S Y V L I 245718 194 Y I P L I S L S I V 24 5719 14 G L S I S T L V T M 23 5720 144A M F S T V G V D L 23 5721 4 F L S M L S A T D L 21 5722 142 L T A M FS T V G V 21 5723 147 S T V G V D L L L I 21 5724 186 H I V A F A I Y YI 21 5725 224 L I S P L M N P V I 21 5726 240 Q I R R A V I K I L 215727 11 T D L G L S I S T L 20 5728 22 T M L S I F W F N V 20 5729 42 HM F F I K F F T V 20 5730 97 M L T P M V A L L I 20 5731 162 L I I R T VL S V A 20 5732 12 D L G L S I S T L V 19 5733 107 R L S Y C H S Q V L19 5734 120 Y C Y H P D V M K L 19 5735 148 T V G V D L L L I L 19 5736157 L L S Y V L I I R T 19 5737 158 L S Y V L I I R T V 19 5738 216 T MI A N T Y L L I 19 5739 15 L S I S T L V T M L 18 5740 51 V M E S S V LL A M 18 5741 156 I L L S Y V L I I R 18 5742 222 Y L L I S P L M N P 185743 49 F T V M E S S V L L 17 5744 86 I G V A S V I R G L 17 5745 87 GV A S V I R G L L 17 5746 89 A S V I R G L L M L 17 5747 94 G L L M L TP M V A 17 5748 189 A F A I Y Y I P L I 17 5749 193 Y Y I P L I S L S I17 5750 232 V I Y S V K T K Q I 17 5751 239 K Q I R R A V I K I 17 575250 T V M E S S V L L A 16 5753 75 A M I L T D S R I A 16 5754 90 S V I RG L L M L T 16 5755 133 D T R I N S A V G L 16 5756 135 R I N S A V G LT A 16 5757 149 V G V D L L L I L L 16 5758 188 V A F A I Y Y I P L 165759 208 K Q A P A Y V H T M 16 5760 215 H T M I A N T Y L L 16 5761 8 LS A T D L G L S I 15 5762 74 Y A M I L T D S R I 15 5763 99 T P M V A LL I R L 15 5764 103 A L L I R L S Y C H 15 5765 131 C T D T R I N S A V15 5766 140 V G L T A M F S T V 15 5767 196 P L I S L S I V H R 15 5768197 L I S L S I V H R F 15 5769 217 M I A N T Y L L I S 15 5770 7 M L SA T D L G L S 14 5771 47 K F F T V M E S S V 14 5772 68 V S N P L R Y AM I 14 5773 83 I A Q I G V A S V I 14 5774 91 V I R G L L M L T P 145775 104 L L I R L S Y C H S 14 5776 106 I R L S Y C H S Q V 14 5777 145M F S T V G V D L L 14 5778 178 E T F S T C V S H I 14 5779 219 A N T YL L I S P L 14 5780 237 K T K Q I R R A V I 14 5781 45 F I K F F T V M ES 13 5782 56 V L L A M A F D R F 13 5783 66 V A V S N P L R Y A 13 578471 P L R Y A M I L T D 13 5785 93 R G L L M L T P M V 13 5786 105 L I RL S Y C H S Q 13 5787 130 S C T D T R I N S A 13 5788 163 I I R T V L SV A S 13 5789 167 V L S V A S P E E R 13 5790 181 S T C V S H I V A F 135791 183 C V S H I V A F A I 13 5792 199 S L S I V H R F G K 13 5793 201S I V H R F G K Q A 13 5794 218 I A N T Y L L I S P 13 5795 228 L M N PV I Y S V K 13 5796 235 S V K T K Q I R R A 13 5797 245 V I K I L H S KE T 13 5798 2 Y Y F L S M L S A T 12 5799 10 A T D L G L S I S T 12 580017 I S T L V T M L S I 12 5801 18 S T L V T M L S I F 12 5802 31 V R E IS F N A C L 12 5803 37 N A C L S H M F F I 12 5804 39 C L S H M F F I KF 12 5805 60 M A F D R F V A V S 12 5806 67 A V S N P L R Y A M 12 580769 S N P L R Y A M I L 12 5808 85 Q I G V A S V I R G 12 5809 115 V L HH S Y C Y H P 12 5810 139 A V G L T A M F S T 12 5811 159 S Y V L I I RT V L 12 5812 170 V A S P E E R K E T 12 5813 205 R F G K Q A P A Y V 125814 209 Q A P A Y V H T M I 12 5815 212 A Y V H T M I A N T 12 5816 23M L S I F W F N V R 11 5817 34 I S F N A C L S H M 11 5818 58 L A M A FD R F V A 11 5819 63 D R F V A V S N P L 11 5820 76 M I L T D S R I A Q11 5821 79 T D S R I A Q I G V 11 5822 98 L T P M V A L L I R 11 5823102 V A L L I R L S Y C 11 5824 128 K L S C T D T R I N 11 5825 136 I NS A V G L T A M 11 5826 146 F S T V G V D L L L 11 5827 179 T F S T C VS H I V 11 5828 236 V K T K Q I R R A V 11 5829 243 R A V I K I L H S K11 5830 9 S A T D L G L S I S 10 5831 16 S I S T L V T M L S 10 5832 19T L V T M L S I F W 10 5833 48 F F T V M E S S V L 10 5834 52 M E S S VL L A M A 10 5835 88 V A S V I R G L L M 10 5836 92 I R G L L M L T P M10 5837 117 H H S Y C Y H P D V 10 5838 126 V M K L S C T D T R 10 5839127 M K L S C T D T R I 10 5840 134 T R I N S A V G L T 10 5841 141 G LT A M F S T V G 10 5842 150 G V D L L L I L L S 10 5843 151 V D L L L IL L S Y 10 5844 160 Y V L I I R T V L S 10 5845 169 S V A S P E E R K E10 5846 182 T C V S H I V A F A 10 5847 214 V H T M I A N T Y L 10 5848220 N T Y L L I S P L M 10 5849 244 A V I K I L H S K E 10 5850 13 L G LS I S T L V T 9 5851 20 L V T M L S I F W F 9 5852 100 P M V A L L I R LS 9 5853 101 M V A L L I R L S Y 9 5854 164 I R T V L S V A S P 9 5855166 T V L S V A S P E E 9 5856 213 Y V H T M I A N T Y 9 5857 3 Y F L SM L S A T D 8 5858 30 N V R E I S F N A C 8 5859 55 S V L L A M A F D R8 5860 65 F V A V S N P L R Y 8 5861 84 A Q I S V A S V I R 8 5862 123 HP D V M K L S C T 8 5863 125 D V M K L S C T D T 8 5864 138 S A V G L TA M F S 8 5865 143 T A M F S T V G V D 8 5866 175 E R K E T F S T C V 85867 187 I V A F A I Y Y I P 8 5868 226 S P L M N P V I Y S 8 5869 229 MN P V I Y S V K T 8 5870 1 M Y Y F L S M L S A 7 5871 33 E I S F N A C LS H 7 5872 72 L R Y A M I L T D S 7 5873 80 D S R I A Q I G V A 7 587481 S R I A Q I G V A S 7 5875 109 S Y C H S Q V L H H 7 5876 110 Y C H SQ V L H H S 7 5877 190 F A I Y Y I P L I S 7 5878 192 I Y Y I P L I S LS 7 5879 202 I V H R F G K Q A P 7 5880 207 G K Q A P A Y V H T 7 5881210 A P A Y V H T M I A 7 5882 242 R R A V I K I L H S 7 5883 21 V T M LS I F W F N 6 5884 41 S H M F F I K F F T 6 5885 61 A F D R F V A V S N6 5886 70 N P L R Y A M I L T 6 5887 78 L T D S R I A Q I G 6 5888 114 QV L H H S Y C Y H 6 5889 122 Y H P D V M K L S C 6 5890 171 A S P E E RK E T F 6 5891 200 L S I V H R F G K Q 6 5892 203 V H R F G K Q A P A 65893 24 L S I F W F N V R E 5 5894 28 W F N V R E I S F N 5 5895 29 F NV R E I S F N A 5 5896 40 L S H M F F I K F F 5 5897 43 M F F I K F F TV M 5 5898 44 F F I K F F T V M E 5 5899 108 L S Y C H S Q V L H 5 5900118 H S Y C Y H P D V M 5 5901 204 H R F G K Q A P A Y 5 5902 230 N P VI Y S V K T K 5 5903 27 F W F N V R E I S F 4 5904 35 S F N A C L S H MF 4 5905 38 A C L S H M F F I K 4 5906 46 I K F F T V M E S S 4 5907 54S S V L L A M A F D 4 5908 62 F D R F V A V S N P 4 5909 73 R Y A M I LT D S R 4 5910 137 N S A V G L T A M F 4 5911 165 R T V L S V A S P E 45912 180 F S T C V S H I V A 4 5913 185 S H I V A F A I Y Y 4 5914 195 IP L I S L S I V H 4 5915 198 I S L S I V H R F G 4 5916 225 I S P L M NP V I Y 4 5917 231 P V I Y S V K T K Q 4 5918 5 L S M L S A T D L G 35919 36 F N A C L S H M F F 3 5920 111 C H S Q V L H H S Y 3 5921 113 SQ V L H H S Y C Y 3 5922 116 L H H S Y C Y H P D 3 5923 119 S Y C Y H PD V M K 3 5924 172 S P E E R K E T F S 3 5925 177 K E T F S T C V S H 35926 184 V S H I V A F A I Y 3 5927 211 P A Y V H T M I A N 3 5928 221 TY L L I S P L M N 3 5929 26 I F W F N V R E I S 2 5930 32 R E I S F N AC L S 2 5931 129 L S C T D T R I N S 2 5932 168 L S V A S P E E R K 25933 173 P E E R K E T F S T 2 5934 233 I Y S V K T K Q I R 2 5935 234 YS V K T K Q I R R 2 5936 238 T K Q I R R A V I K 2 5937 241 I R R A V IK I L H 2 5938 64 R F V A V S N P L R 1 5939 121 C Y H P D V M K L S 15940 132 T D T R I N S A V G 1 5941 206 F G K Q A P A Y V H 1 5942 124 PD V M K L S C T D −1 5943 174 E E R K E T F S T C −1 5944 176 R K E T FS T C V S −1 5945 53 E S S V L L A M A F −2 5946 HLA-A*0202 10-mers v.1:238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 59 A M A F D R F V A V 45947 189 A F A I Y Y I P L I 4 5948 210 A P A Y V H T M I A 4 5949 8 L SA T D L G L S I 3 5950 36 F N A C L S H M F F 3 5951 57 L L A M A F D RF V 3 5952 65 F V A V S N P L R Y 3 5953 73 R Y A M I L T D S R 3 595482 R I A Q I G V A S V 3 5955 87 G V A S V I R G L L 3 5956 101 M V A LL I R L S Y 3 5957 137 N S A V G L T A M F 3 5958 142 L T A M F S T V GV 3 5959 169 S V A S P E E R K E 3 5960 187 I V A F A I Y Y I P 3 5961208 K Q A P A Y V H T M 3 5962 217 M I A N T Y L L I S 3 5963 242 R R AV I K I L H S 3 5964 9 S A T D L G L S I S 2 5965 37 N A C L S H M F F I2 5966 58 L A M A F D R F V A 2 5967 60 M A F D R F V A V S 2 5968 66 VA V S N P L R Y A 2 5969 74 Y A M I L T D S R I 2 5970 83 I A Q I G V AS V I 2 5971 88 V A S V I R G L L M 2 5972 102 V A L L I R L S Y C 25973 138 S A V G L T A M F S 2 5974 143 T A M F S T V G V D 2 5975 170 VA S P E E R K E T 2 5976 188 V A F A I Y Y I P L 2 5977 190 F A I Y Y IP L I S 2 5978 209 Q A P A Y V H T M I 2 5979 211 P A Y V H T M I A N 25980 218 I A N T Y L L I S P 2 5981 243 R A V I K I L H S K 2 5982 10 AT D L G L S I S T 1 5983 38 A C L S H M F F I K 1 5984 61 A F D R F V AV S N 1 5985 67 A V S N P L R Y A M 1 5986 75 A M I L T D S R I A 1 598784 A Q I G V A S V I R 1 5988 89 A S V I R G L L M L 1 5989 103 A L L IR L S Y C H 1 5990 139 A V G L T A M F S T 1 5991 144 A M F S T V G V DL 1 5992 171 A S P E E R K E T F 1 5993 191 A I Y Y I P L I S L 1 5994212 A Y V H T M I A N T 1 5995 219 A N T Y L L I S P L 1 5996 244 A V IK I L H S K E 1 5997 HLA-A*0203 10-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 89 0 score SEQ ID 52 M E S S V L L A M A 18 5998 182 T C V S H I V A F A18 5999 203 V H R F G K Q A P A 18 6000 1 M Y Y F L S M L S A 10 6001 29F N V R E I S F N A 10 6002 50 T V M E S S V L L A 10 6003 58 L A M A FD R F V A 10 6004 66 V A V S N P L R Y A 10 6005 75 A M I L T D S R I A10 6006 80 D S R I A Q I G V A 10 6007 94 G L L M L T P M V A 10 6008130 S C T D T R I N S A 10 6009 135 R I N S A V G L T A 10 6010 162 L II R T V L S V A 10 6011 180 F S T C V S H I V A 10 6012 201 S I V H R FG K Q A 10 6013 210 A P A Y V H T M I A 10 6014 235 S V K T K Q I R R A10 6015 2 Y Y F L S M L S A T 9 6016 30 N V R E I S F N A C 9 6017 51 VM E S S V L L A M 9 6018 53 E S S V L L A M A F 9 6019 59 A M A F D R FV A V 9 6020 67 A V S N P L R Y A M 9 6021 76 M I L T D S R I A Q 9 602281 S R I A Q I G V A S 9 6023 95 L L M L T P M V A L 9 6024 131 C T D TR I N S A V 9 6025 136 I N S A V G L T A M 9 6026 163 I I R T V L S V AS 9 6027 181 S T C V S H I V A F 9 6028 183 C V S H I V A F A I 9 6029202 I V H R F G K Q A P 9 6030 204 H R F G K Q A P A Y 9 6031 211 P A YV H T M I A N 9 6032 236 V K T K Q I R R A V 9 6033 3 Y F L S M L S A TD 8 6034 31 V R E I S F N A C L 8 6035 54 S S V L L A M A F D 8 6036 60M A F D R F V A V S 8 6037 68 V S N P L R Y A M I 8 6038 77 I L T D S RI A Q I 8 6039 82 R I A Q I G V A S V 8 6040 96 L M L T P M V A L L 86041 132 T D T R I N S A V G 8 6042 137 N S A V G L T A M F 8 6043 164 IR T V L S V A S P 8 6044 184 V S H I V A F A I Y 8 6045 205 R F G K Q AP A Y V 8 6046 212 A Y V H T M I A N T 8 6047 237 K T K Q I R R A V I 86048 8/25 HLA-A1 10-mers v.1: 237P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQID 184 V S H I V A F A I Y 23 6049 65 F V A V S N P L R Y 22 6050 101 MV A L L I R L S Y 22 6051 151 V D L L L I L L S Y 22 6052 10 A T D L G LS I S T 21 6053 185 S H I V A F A I Y Y 21 6054 225 I S P L M N P V I Y19 6055 150 G V D L L L I L L S 18 6056 51 V M E S S V L L A M 17 6057113 S Q V L H H S Y C Y 17 6058 131 C T D T R I N S A V 17 6059 147 S TV G V D L L L I 17 6060 213 Y V H T M I A N T Y 17 6061 78 L T D S R I AQ I G 16 6062 204 H R F G K Q A P A Y 16 6063 111 C H S Q V L H H S Y 156064 97 M L T P M V A L L I 13 6065 146 F S T V G V D L L L 13 6066 31 VR E I S F N A C L 12 6067 89 A S V I R G L L M L 12 6068 98 L T P M V AL L I R 12 6069 172 S P E E R K E T F S 12 6070 193 Y Y I P L I S L S I12 6071 8 L S A T D L G L S I 11 6072 61 A F D R F V A V S N 11 6073 176R K E T F S T C V S 11 6074 17 I S T L V T M L S I 10 6075 21 V T M L SI F W F N 10 6076 39 C L S H M F F I K F 10 6077 68 V S N P L R Y A M I10 6078 88 V A S V I R G L L M 10 6079 123 H P D V M K L S C T 10 6080173 P E E R K E T F S T 10 6081 180 F S T C V S H I V A 10 6082 234 Y SV K T K Q I R R 10 6083 49 F T V M E S S V L L 9 6084 50 T V M E S S V LL A 9 6085 109 S Y C H S Q V L H H 9 6086 129 L S C T D T R I N S 9 6087161 V L I I R T V L S V 9 6088 200 L S I V H R F G K Q 9 6089 6 S M L SA T D L G L 8 6090 18 S T L V T M L S I F 8 6091 91 V I R G L L M L T P8 6092 122 Y H P D V M K L S C 8 6093 181 S T C V S H I V A F 8 6094 215H T M I A N T Y L L 8 6095 216 T M I A N T Y L L I 8 6096 220 N T Y L LI S P L M 8 6097 237 K T K Q I R R A V I 8 6098 13 L G L S I S T L V T 76099 71 P L R Y A M I L T D 7 6100 135 R I N S A V G L T A 7 6101 149 VG V D L L L I L L 7 6102 155 L I L L S Y V L I I 7 6103 178 E T F S T CV S H I 7 6104 190 F A I Y Y I P L I S 7 6105 221 T Y L L I S P L M N 76106 226 S P L M N P V I Y S 7 6107 239 K Q I R R A V I K I 7 6108 1 M YY F L S M L S A 6 6109 5 L S M L S A T D L G 6 6110 15 L S I S T L V T ML 6 6111 33 E I S F N A C L S H 6 6112 54 S S V L L A M A F D 6 6113 70N P L R Y A M I L T 6 6114 108 L S Y C H S Q V L H 6 6115 121 C Y H P DV M K L S 6 6116 133 D T R I N S A V G L 6 6117 142 L I A M F S T V G V6 6118 148 T V G V D L L L I L 6 6119 165 R I V L S V A S P E 6 6120 170V A S P E E R K E T 6 6121 217 M I A N T Y L L I S 6 6122 224 L I S P LM N P V I 6 6123 241 I R R A V I K I L H 6 6124 242 R R A V I K I L H S6 6125 19 T L V T M L S I F W 5 6126 23 M L S I F W F N V R 5 6127 24 LS I F W F N V R E 5 6128 27 F W F N V R E I S F 5 6129 56 V L L A M A FD R F 5 6130 76 M I L T D S R I A Q 5 6131 80 D S R I A Q I G V A 5 613285 Q I G V A S V I R G 5 6133 118 H S Y C Y H P D V M 5 6134 120 Y C Y HP D V M K L 5 6135 137 N S A V G L T A M F 5 6136 156 I L L S Y V L I IR 5 6137 157 L L S Y V L I I R T 5 6138 171 A S P E E R K E T F 5 6139188 V A F A I Y Y I P L 5 6140 191 A I Y Y I P L I S L 5 6141 195 I P LI S L S I V H 5 6142 208 K Q A P A Y V H T M 5 6143 228 L M N P V I Y SV K 5 6144 16 S I S T L V T M L S 4 6145 34 I S F N A C L S H M 4 614638 A C L S H M F F I K 4 6147 40 L S H M F F I K F F 4 6148 43 M F F I KF F T V M 4 6149 53 E S S V L L A M A F 4 6150 59 A M A F D R F V A V 46151 79 T D S R I A Q I G V 4 6152 90 S V I R G L L M L T 4 6153 99 T PM V A L L I R L 4 6154 112 H S Q V L H H S Y C 4 6155 140 V G L T A M FS T V 4 6156 158 L S Y V L I I R T V 4 6157 159 S Y V L I I R T V L 46158 160 Y V L I I R T V L S 4 6159 168 L S V A S P E E R K 4 6160 169 SV A S P E E R K E 4 6161 198 I S L S I V H R F G 4 6162 199 S L S I V HR F G K 4 6163 211 P A Y V H T M I A N 4 6164 218 I A N T Y L L I S P 46165 7 M L S A T D L G L S 3 6166 12 D L G L S I S T L V 3 6167 25 S I FW F N V R E I 3 6168 30 N V R E I S F N A C 3 6169 35 S F N A C L S H MF 3 6170 42 H M F F I K F F T V 3 6171 64 R F V A V S N P L R 3 6172 81S R I A Q I G V A S 3 6173 87 G V A S V I R G L L 3 6174 96 L M L T P MV A L L 3 6175 119 S Y C Y H P D V M K 3 6176 134 T R I N S A V G L T 36177 138 S A V G L T A M F S 3 6178 145 M F S T V G V D L L 3 6179 154 LL I L L S Y V L I 3 6180 174 E E R K E T F S T C 3 6181 189 A F A I Y YI P L I 3 6182 201 S I V H R F G K Q A 3 6183 222 Y L L I S P L M N P 36184 244 A V I K I L H S K E 3 6185 2 Y Y F L S M L S A T 2 6186 3 Y F LS M L S A T D 2 6187 4 F L S M L S A T D L 2 6188 9 S A T D L G L S I S2 6189 32 R E I S F N A C L S 2 6190 41 S H M F F I K F F T 2 6191 44 FF I K F F T V M E 2 6192 45 F I K F F T V M E S 2 6193 48 F F T V M E SS V L 2 6194 55 S V L L A M A F D R 2 6195 58 L A M A F D R F V A 2 619660 M A F D R F V A V S 2 6197 62 F D R F V A V S N P 2 6198 67 A V S N PL R Y A M 2 6199 69 S N P L R Y A M I L 2 6200 74 Y A M I L T D S R I 26201 84 A Q I G V A S V I R 2 6202 94 G L L M L T P M V A 2 6203 100 P MV A L L I R L S 2 6204 103 A L L I R L S Y C H 2 6205 107 R L S Y C H SQ V L 2 6206 110 Y C H S Q V L H H S 2 6207 115 V L H H S Y C Y H P 26208 130 S C T D T R I N S A 2 6209 141 G L T A M F S T V G 2 6210 143 TA M F S T V G V D 2 6211 144 A M F S T V G V D L 2 6212 153 L L L I L LS Y V L 2 6213 167 V L S V A S P E E R 2 6214 192 I Y Y I P L I S L S 26215 194 Y I P L I S L S I V 2 6216 206 F G K Q A P A Y V H 2 6217 214 VH T M I A N T Y L 2 6218 229 M N P V I Y S V K T 2 6219 231 P V I Y S VK T K Q 2 6220 235 S V K T K Q I R R A 2 6221 236 V K T K Q I R R A V 26222 11 T D L G L S I S T L 1 6223 14 G L S I S T L V T M 1 6224 26 I FW F N V R E I S 1 6225 29 F N V R E I S F N A 1 6226 36 F N A C L S H MF F 1 6227 52 M E S S V L L A M A 1 6228 57 L L A M A F D R F V 1 622966 V A V S N P L R Y A 1 6230 75 A M I L T D S R I A 1 6231 77 I L T D SR I A Q I 1 6232 82 R I A Q I G V A S V 1 6233 83 I A Q I G V A S V I 16234 93 R G L L M L T P M V 1 6235 95 L L M L T P M V A L 1 6236 102 V AL L I R L S Y C 1 6237 104 L L I R L S Y C H S 1 6238 126 V M K L S C TD T R 1 6239 128 K L S C T D T R I N 1 6240 132 T D T R I N S A V G 16241 139 A V G L T A M F S T 1 6242 152 D L L L I L L S Y V 1 6243 162 LI I R T V L S V A 1 6244 164 I R T V L S V A S P 1 6245 182 T C V S H IV A F A 1 6246 196 P L I S L S I V H R 1 6247 197 L I S L S I V H R F 16248 203 V H R F G K Q A P A 1 6249 209 Q A P A Y V H T M I 1 6250 210 AP A Y V H T M I A 1 6251 212 A Y V H T M I A N T 1 6252 219 A N T Y L LI S P L 1 6253 223 L L I S P L M N P V 1 6254 227 P L M N P V I Y S V 16255 230 N P V I Y S V K T K 1 6256 232 V I Y S V K T K Q I 1 6257 245 VI K I L H S K E T 1 6258 HLA-A26 10-mers v.1: 238P1B2 Pos 1 2 3 4 5 6 78 9 0 score SEQ ID 133 D T R I N S A V G L 26 6259 181 S T C V S H I V AF 26 6260 18 S T L V T M L S I F 25 6261 178 E T F S T C V S H I 25 6262197 L I S L S I V H R F 25 6263 20 L V T M L S I F W F 24 6264 39 C L SH M F F I K F 23 6265 56 V L L A M A F D R F 23 6266 191 A I Y Y I P L IS L 23 6267 65 F V A V S N P L R Y 22 6268 95 L L M L T P M V A L 226269 101 M V A L L I R L S Y 22 6270 148 T V G V D L L L I L 22 6271 240Q I R R A V I K I L 22 6272 14 G L S I S T L V T M 21 6273 43 M F F I KF F T V M 20 6274 87 G V A S V I R G L L 20 6275 213 Y V H T M I A N T Y20 6276 49 F T V M E S S V L L 19 6277 67 A V S N P L R Y A M 19 6278152 D L L L I L L S Y V 19 6279 220 N T Y L L I S P L M 19 6280 53 E S SV L L A M A F 18 6281 82 R I A Q I G V A S V 18 6282 145 M F S T V G V DL L 18 6283 215 H T M I A N T Y L L 18 6284 25 S I F W F N V R E I 176285 30 N V R E I S F N A C 17 6286 33 E I S F N A C L S H 17 6287 35 SF N A C L S H M F 17 6288 45 F I K F F T V M E S 17 6289 90 S V I R G LL M L T 17 6290 107 R L S Y C H S Q V L 17 6291 125 D V M K L S C T D T17 6292 162 L I I R T V L S V A 17 6293 196 P L I S L S I V H R 17 62944 F L S M L S A T D L 16 6295 15 L S I S T L V T M L 16 6296 34 I S F NA C L S H M 16 6297 50 T V M E S S V L L A 16 6298 63 D R F V A V S N PL 16 6299 91 V I R G L L M L T P 16 6300 147 S T V G V D L L L I 16 6301153 L L L I L L S Y V L 16 6302 194 Y I P L I S L S I V 16 6303 204 H RF G K Q A P A Y 16 6304 235 S V K T K Q I R R A 16 6305 11 T D L G L S IS T L 15 6306 48 F F T V M E S S V L 15 6307 77 I L T D S R I A Q I 156308 85 Q I G V A S V I R G 15 6309 98 L T P M V A L L I R 15 6310 104 LL I R L S Y C H S 15 6311 139 A V G L T A M F S T 15 6312 150 G V D L LL I L L S 15 6313 151 V D L L L I L L S Y 15 6314 154 L L I L L S Y V LI 15 6315 161 V L I I R T V L S V 15 6316 184 V S H I V A F A I Y 156317 187 I V A F A I Y Y I P 15 6318 208 K Q A P A Y V H T M 15 6319 217M I A N T Y L L I S 15 6320 223 L L I S P L M N P V 15 6321 244 A V I KI L H S K E 15 6322 12 D L G L S I S T L V 14 6323 21 V T M L S I F W FN 14 6324 40 L S H M F F I K F F 14 6325 51 V M E S S V L L A M 14 6326114 Q V L H H S Y C Y H 14 6327 120 Y C Y H P D V M K L 14 6328 155 L IL L S Y V L I I 14 6329 186 H I V A F A I Y Y I 14 6330 188 V A F A I YY I P L 14 6331 222 Y L L I S P L M N P 14 6332 27 F W F N V R E I S F13 6333 78 L T D S R I A Q I G 13 6334 86 I G V A S V I R G L 13 6335 89A S V I R G L L M L 13 6336 96 L M L T P M V A L L 13 6337 99 T P M V AL L I R L 13 6338 131 C T D T R I N S A V 13 6339 136 I N S A V G L T AM 13 6340 137 N S A V G L T A M F 13 6341 142 L T A M F S T V G V 136342 149 V G V D L L L I L L 13 6343 156 I L L S Y V L I I R 13 6344 157L L S Y V L I I R T 13 6345 166 T V L S V A S P E E 13 6346 169 S V A SP E E R K E 13 6347 171 A S P E E R K E T F 13 6348 219 A N T Y L L I SP L 13 6349 224 L I S P L M N P V I 13 6350 227 P L M N P V I Y S V 136351 231 P V I Y S V K T K Q 13 6352 237 K T K Q I R R A V I 13 6353 7 ML S A T D L G L S 12 6354 10 A T D L G L S I S T 12 6355 23 M L S I F WF N V R 12 6356 36 F N A C L S H M F F 12 6357 71 P L R Y A M I L T D 126358 92 I R G L L M L T P M 12 6359 111 C H S Q V L H H S Y 12 6360 144A M F S T V G V D L 12 6361 163 I I R T V L S V A S 12 6362 174 E E R KE T F S T C 12 6363 185 S H I V A F A I Y Y 12 6364 189 A F A I Y Y I PL I 12 6365 202 I V H R F G K Q A P 12 6366 225 I S P L M N P V I Y 126367 232 V I Y S V K T K Q I 12 6368 245 V I K I L H S K E T 12 6369 16S I S T L V T M L S 11 6370 28 W F N V R E I S F N 11 6371 44 F F I K FF T V M E 11 6372 76 M I L I D S R I A Q 11 6373 105 L I R L S Y C H S Q11 6374 135 R I N S A V G L T A 11 6375 160 Y V L I I R T V L S 11 6376165 R T V L S V A S P E 11 6377 183 C V S H I V A F A I 11 6378 201 S IV H R F G K Q A 11 6379 6 S M L S A T D L G L 10 6380 47 K F F T V M E SS V 10 6381 55 S V L L A M A F D R 10 6382 69 S N P L R Y A M I L 106383 80 D S R I A Q I G V A 10 6384 97 M L T P M V A L L I 10 6385 113 SQ V L H H S Y C Y 10 6386 31 V R E I S F N A C L 9 6387 57 L L A M A F DR F V 9 6388 61 A F D R F V A V S N 9 6389 94 G L L M L T P M V A 9 6390115 V L H H S Y C Y H P 9 6391 167 V L S V A S P E E R 9 6392 175 E R KE T F S T C V 9 6393 199 S L S I V H R F G K 9 6394 2 Y Y F L S M L S AT 8 6395 3 Y F L S M L S A T D 8 6396 19 T L V T M L S I F W 8 6397 60 MA F D R F V A V S 8 6398 68 V S N P L R Y A M I 8 6399 88 V A S V I R GL L M 8 6400 103 A L L I R L S Y C H 8 6401 118 H S Y C Y H P D V M 86402 128 K L S C T D T R I N 8 6403 141 G L T A M F S T V G 8 6404 146 FS T V G V D L L L 8 6405 159 S Y V L I I R T V L 8 6406 205 R F G K Q AP A Y V 8 6407 214 V H T M I A N T Y L 8 6408 46 I K F F T V M E S S 76409 52 M E S S V L L A M A 7 6410 59 A M A F D R F V A V 7 6411 64 R FV A V S N P L R 7 6412 200 L S I V H R F G K Q 7 6413 228 L M N P V I YS V K 7 6414 239 K Q I R R A V I K I 7 6415 9 S A T D L G L S I S 6 641626 I F W F N V R E I S 6 6417 42 H M F F I K F F I V 6 6418 62 F D R F VA V S N P 6 6419 110 Y C H S Q V L H H S 6 6420 121 C Y H P D V M K L S6 6421 123 H P D V M K L S C T 6 6422 130 S C T D T R I N S A 6 6423 134T R I N S A V G L T 6 6424 164 I R T V L S V A S P 6 6425 179 T F S T CV S H I V 6 6426 182 T C V S H I V A F A 6 6427 207 G K Q A P A Y V H T6 6428 212 A Y V H T M I A N T 6 6429 216 T M I A N I Y L L I 6 6430 242R R A V I K I L H S 6 6431 1 M Y Y F L S M L S A 5 6432 17 I S T L V T ML S I 5 6433 38 A C L S H M F F I K 5 6434 54 S S V L L A M A F D 5 643566 V A V S N P L R Y A 5 6436 84 A Q I G V A S V I R 5 6437 102 V A L LI R L S Y C 5 6438 109 S Y C H S Q V L H H 5 6439 116 L H H S Y C Y H PD 5 6440 140 V G L T A M F S T V 5 6441 192 I Y Y I P L I S L S 5 6442193 Y Y I P L I S L S I 5 6443 211 P A Y V H T M I A N 5 6444 218 I A NT Y L L I S P 5 6445 243 R A V I K I L H S K 5 6446 24 L S I F W F N V RE 4 6447 37 N A C L S H M F F I 4 6448 70 N P L R Y A M I L T 4 6449 72L R Y A M I L T D S 4 6450 81 S R I A Q I G V A S 4 6451 100 P M V A L LI R L S 4 6452 143 T A M F S T V G V D 4 6453 158 L S Y V L I I R T V 46454 226 S P L M N P V I Y S 4 6455 230 N P V I Y S V K T K 4 6456 32 RE I S F N A C L S 3 6457 106 I R L S Y C H S Q V 3 6458 122 Y H P D V MK L S C 3 6459 138 S A V G L T A M F S 3 6460 170 V A S P E E R K E T 36461 229 M N P V I Y S V K T 3 6462 8 L S A T D L G L S I 2 6463 22 T ML S I F W F N V 2 6464 73 R Y A M I L T D S R 2 6465 74 Y A M I L T D SR I 2 6466 75 A M I L T D S R I A 2 6467 93 R G L L M L T P M V 2 6468119 S Y C Y H P D V M K 2 6469 127 M K L S C T D T R I 2 6470 172 S P EE R K E T F S 2 6471 177 K E T F S T C V S H 2 6472 190 F A I Y Y I P LI S 2 6473 206 F G K Q A P A Y V H 2 6474 209 Q A P A Y V H T M I 2 6475210 A P A Y V H T M I A 2 6476 234 Y S V K T K Q I R R 2 6477 236 V K TK Q I R R A V 2 6478 13 L G L S I S T L V T 1 6479 29 F N V R E I S F NA 1 6480 79 T D S R I A Q I G V 1 6481 83 I A Q I G V A S V I 1 6482 108L S Y C H S Q V L H 1 6483 112 H S Q V L H H S Y C 1 6484 117 H H S Y CY H P D V 1 6485 126 V M K L S C T D T R 1 6486 129 L S C T D T R I N S1 6487 132 T D T R I N S A V G 1 6488 168 L S V A S P E E R K 1 6489 173P E E R K E T F S T 1 6490 198 I S L S I V H R F G 1 6491 203 V H R F SK Q A P A 1 6492 221 T Y L L I S P L M N 1 6493 233 I Y S V K T K Q I R1 6494 238 T K Q I R R A V I K 1 6495 HLA-A3 10-mers v.1: 238P1B2 Pos 12 3 4 5 6 7 8 9 0 score SEQ ID 101 M V A L L I R L S Y 24 6496 199 S L SI V H R F G K 23 6497 213 Y V H T M I A N T Y 23 6498 135 R I N S A V GL T A 22 6499 55 S V L L A M A F D R 21 6500 65 F V A V S N P L R Y 216501 162 L I I R T V L S V A 21 6502 196 P L I S L S I V H R 21 6503 71P L R Y A M I L T D 20 6504 91 V I R G L L M L T P 20 6505 103 A L L I RL S Y C H 20 6506 228 L M N P V I Y S V K 20 6507 14 G L S I S T L V T M19 6508 23 M L S I F W F N V R 19 6509 77 I L T D S R I A Q I 19 6510 97M L T P M V A L L I 19 6511 161 V L I I R I V L S V 19 6512 244 A V I KI L H S K E 19 6513 56 V L L A M A F D R F 18 6514 82 R I A Q I G V A SV 18 6515 90 S V I R G L L M L T 18 6516 94 G L L M L T P M V A 18 6517107 R L S Y C H S Q V L 18 6518 114 Q V L H H S Y C Y H 18 6519 154 L LI L L S Y V L I 18 6520 156 I L L S Y V L I I R 18 6521 163 I I R T V LS V A S 18 6522 238 T K Q I R R A V I K 18 6523 33 E I S F N A C L S H17 6524 141 G L T A M F S T V G 17 6525 153 L L L I L L S Y V L 17 6526160 Y V L I I R T V L S 17 6527 191 A I Y Y I P L I S L 17 6528 243 R AV I K I L H S K 17 6529 67 A V S N P L R Y A M 16 6530 84 A Q I G V A SV I R 16 6531 95 L L M L T P M V A L 16 6532 104 L L I R L S Y C H S 166533 119 S Y C Y H P D V M K 16 6534 139 A V G L T A M F S T 16 6535 152D L L L I L L S Y V 16 6536 202 I V H R F G K Q A P 16 6537 240 Q I R RA V I K I L 16 6538 20 L V T M L S I F W F 15 6539 30 N V R E I S F N AC 15 6540 38 A C L S H M F F I K 15 6541 61 A F D R F V A V S N 15 6542167 V L S V A S P E E R 15 6543 201 S I V H R F G K Q A 15 6544 224 L IS P L M N P V I 15 6545 230 N P V I Y S V K T K 15 6546 232 V I Y S V KT K Q I 15 6547 4 F L S M L S A T D L 14 6548 39 C L S H M F F I K F 146549 50 T V M E S S V L L A 14 6550 81 S R I A Q I G V A S 14 6551 105 LI R L S Y C H S Q 14 6552 150 G V D L L L I L L S 14 6553 151 V D L L LI L L S Y 14 6554 155 L I L L S Y V L I I 14 6555 183 C V S H I V A F AI 14 6556 222 Y L L I S P L M N P 14 6557 225 I S P L M N P V I Y 146558 231 P V I Y S V K T K Q 14 6559 7 M L S A T D L G L S 13 6560 83 IA Q I G V A S V I 13 6561 87 G V A S V I R G L L 13 6562 128 K L S C T DT R I N 13 6563 148 T V G V D L L L I L 13 6564 177 K E T F S T C V S H13 6565 185 S H I V A F A I Y Y 13 6566 187 I V A F A I Y Y I P 13 6567195 I P L I S L S I V H 13 6568 197 L I S L S I V H R F 13 6569 217 M IA N T Y L L I S 13 6570 223 L L I S P L M N P V 13 6571 227 P L M N P VI Y S V 13 6572 12 D L G L S I S T L V 12 6573 76 M I L T D S R I A Q 126574 108 L S Y C H S Q V L H 12 6575 166 T V L S V A S P E E 12 6576 168L S V A S P E E R K 12 6577 169 S V A S P E E R K E 12 6578 171 A S P EE R K E T F 12 6579 194 Y I P L I S L S I V 12 6580 204 H R F G K Q A PA Y 12 6581 206 F G K Q A P A Y V H 12 6582 235 S V K T K Q I R R A 126583 237 K T K Q I R R A V I 12 6584 11 T D L G L S I S T L 11 6585 57 LL A M A F D R F V 11 6586 73 R Y A M I L T D S R 11 6587 125 D V M K L SC T D T 11 6588 133 D T R I N S A V G L 11 6589 165 R T V L S V A S P E11 6590 193 Y Y I P L I S L S I 11 6591 208 K Q A P A Y V H T M 11 6592241 I R R A V I K I L H 11 6593 16 S I S T L V T M L S 10 6594 18 S T LV T M L S I F 10 6595 19 T L V T M L S I F W 10 6596 32 R E I S F N A CL S 10 6597 45 F I K F F T V M E S 10 6598 64 R F V A V S N P L R 106599 85 Q I G V A S V I R G 10 6600 106 I R L S Y C H S Q V 10 6601 115V L H H S Y C Y H P 10 6602 126 V M K L S C T D T R 10 6603 132 T D T RI N S A V G 10 6604 144 A M F S T V G V D L 10 6605 157 L L S Y V L I IR T 10 6606 174 E E R K E T F S T C 10 6607 181 S T C V S H I V A F 106608 184 V S H I V A F A I Y 10 6609 186 H I V A F A I Y Y I 10 6610 192I Y Y I P L I S L S 10 6611 245 V I K I L H S K E T 10 6612 1 M Y Y F LS M L S A 9 6613 3 Y F L S M L S A T D 9 6614 8 L S A T D L G L S I 96615 13 L G L S I S T L V T 9 6616 25 S I F W F N V R E I 9 6617 53 E SS V L L A M A F 9 6618 59 A M A F D R F V A V 9 6619 80 D S R I A Q I GV A 9 6620 118 H S Y C Y H P D V M 9 6621 137 N S A V G L T A M F 9 6622140 V G L T A M F S T V 9 6623 239 K Q I R R A V I K I 9 6624 17 I S T LV T M L S I 8 6625 35 S F N A C L S H M F 8 6626 44 F F I K F F T V M E8 6627 47 K F F T V M E S S V 8 6628 60 M A F D R F V A V S 8 6629 89 AS V I R G L L M L 8 6630 93 R G L L M L T P M V 8 6631 109 S Y C H S Q VL H H 8 6632 111 C H S Q V L H H S Y 8 6633 113 S Q V L H H S Y C Y 86634 158 L S Y V L I I R T V 8 6635 159 S Y V L I I R T V L 8 6636 176 RK E T F S T C V S 8 6637 205 R F G K Q A P A Y V 8 6638 216 T M I A N TY L L I 8 6639 221 T Y L L I S P L M N 8 6640 242 R R A V I K I L H S 86641 24 L S I F W F N V R E 7 6642 27 F W F N V R E I S F 7 6643 48 F FT V M E S S V L 7 6644 58 L A M A F D R F V A 7 6645 68 V S N P L R Y AM I 7 6646 72 L R Y A M I L T D S 7 6647 75 A M I L T D S R I A 7 664898 L T P M V A L L I R 7 6649 138 S A V G L T A M F S 7 6650 164 I R T VL S V A S P 7 6651 190 F A I Y Y I P L I S 7 6652 6 S M L S A T D L G L6 6653 10 A T D L G L S I S T 6 6654 34 I S F N A C L S H M 6 6655 36 FN A C L S H M F F 6 6656 43 M F F I K F F T V M 6 6657 62 F D R F V A VS N P 6 6658 69 S N P L R Y A M I L 6 6659 88 V A S V I R G L L M 6 6660102 V A L L I R L S Y C 6 6661 122 Y H P D V M K L S C 6 6662 136 I N SA V G L T A M 6 6663 147 S T V G V D L L L I 6 6664 203 V H R F G K Q AP A 6 6665 207 G K Q A P A Y V H T 6 6666 209 Q A P A Y V H T M I 6 6667212 A Y V H T M I A N T 6 6668 219 A N T Y L L I S P L 6 6669 233 I Y SV K T K Q I R 6 6670 2 Y Y F L S M L S A T 5 6671 9 S A T D L G L S I S5 6672 15 L S I S T L V T M L 5 6673 54 S S V L L A M A F D 5 6674 70 NP L R Y A M I L T 5 6675 96 L M L T P M V A L L 5 6676 120 Y C Y H P D VM K L 5 6677 134 T R I N S A V G L T 5 6678 142 L T A M F S T V G V 56679 143 T A M F S T V G V D 5 6680 173 P E E R K E T F S T 5 6681 189 AF A I Y Y I P L I 5 6682 210 A P A Y V H T M I A 5 6683 211 P A Y V H TM I A N 5 6684 220 N T Y L L I S P L M 5 6685 31 V R E I S F N A C L 46686 40 L S H M F F I K F F 4 6687 42 H M F F I K F F T V 4 6688 46 I KF F T V M E S S 4 6689 49 F T V M E S S V L L 4 6690 51 V M E S S V L LA M 4 6691 52 M E S S V L L A M A 4 6692 74 Y A M I L T D S R I 4 669386 I G V A S V I R G L 4 6694 92 I R G L L M L T P M 4 6695 124 P D V MK L S C T D 4 6696 130 S C T D T R I N S A 4 6697 131 C T D T R I N S AV 4 6698 170 V A S P E E R K E T 4 6699 180 F S T C V S H I V A 4 6700198 I S L S I V H R F G 4 6701 200 L S I V H R F G K Q 4 6702 218 I A NT Y L L I S P 4 6703 229 M N P V I Y S V K T 4 6704 234 Y S V K T K Q IR R 4 6705 26 I F W F N V R E I S 3 6706 28 W F N V R E I S F N 3 670729 F N V R E I S F N A 3 6708 78 L T D S R I A Q I G 3 6709 79 T D S R IA Q I G V 3 6710 112 H S Q V L H H S Y C 3 6711 121 C Y H P D V M K L S3 6712 123 H P D V M K L S C T 3 6713 127 M K L S C T D T R I 3 6714 146F S T V G V D L L L 3 6715 172 S P E E R K E T F S 3 6716 175 E R K E TF S T C V 3 6717 178 E T F S T C V S H I 3 6718 182 T C V S H I V A F A3 6719 226 S P L M N P V I Y S 3 6720 22 T M L S I F W F N V 2 6721 100P M V A L L I R L S 2 6722 188 V A F A I Y Y I P L 2 6723 236 V K T K QI R R A V 2 6724 5 L S M L S A T D L G 1 6725 21 V T M L S I F W F N 16726 37 N A C L S H M F F I 1 6727 41 S H M F F I K F F T 1 6728 129 L SC T D T R I N S 1 6729 149 V G V D L L L I L L 1 6730 214 V H T M I A NT Y L 1 6731 215 H T M I A N T Y L L 1 6732 HLA-B*0702 10-mers v.1:238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 99 T P M V A L L I R L 216733 210 A P A Y V H T M I A 20 6734 123 H P D V M K L S C T 17 6735 70N P L R Y A M I L T 16 6736 89 A S V I R G L L M L 14 6737 95 L L M L TP M V A L 14 6738 107 R L S Y C H S Q V L 14 6739 133 D T R I N S A V GL 14 6740 144 A M F S T V G V D L 14 6741 4 F L S M L S A T D L 13 674259 A M A F D R F V A V 13 6743 145 M F S T V G V D L L 13 6744 148 T V GV D L L L I L 13 6745 159 S Y V L I I R T V L 13 6746 219 A N T Y L L IS P L 13 6747 6 S M L S A T D L G L 12 6748 11 T D L G L S I S T L 126749 15 L S I S T L V T M L 12 6750 49 F T V M E S S V L L 12 6751 67 AV S N P L R Y A M 12 6752 86 I G V A S V I R G L 12 6753 87 G V A S V IR G L L 12 6754 96 L M L T P M V A L L 12 6755 136 I N S A V G L T A M12 6756 146 F S T V G V D L L L 12 6757 172 S P E E R K E T F S 12 6758188 V A F A I Y Y I P L 12 6759 191 A I Y Y I P L I S L 12 6760 195 I PL I S L S I V H 12 6761 215 H T M I A N T Y L L 12 6762 240 Q I R R A VI K I L 12 6763 31 V R E I S F N A C L 11 6764 48 F F T V M E S S V L 116765 63 D R F V A V S N P L 11 6766 120 Y C Y H P D V M K L 11 6767 153L L L I L L S Y V L 11 6768 214 V H T M I A N T Y L 11 6769 224 L I S PL M N P V I 11 6770 226 S P L M N P V I Y S 11 6771 230 N P V I Y S V KT K 11 6772 13 L G L S I S T L V T 10 6773 14 G L S I S T L V T M 106774 50 T V M E S S V L L A 10 6775 53 E S S V L L A M A F 10 6776 58 LA M A F D R F V A 10 6777 69 S N P L R Y A M I L 10 6778 82 R I A Q I GV A S V 10 6779 88 V A S V I R G L L M 10 6780 92 I R G L L M L T P M 106781 142 L T A M F S T V G V 10 6782 147 S T V G V D L L L I 10 6783 149V G V D L L L I L L 10 6784 170 V A S P E E R K E T 10 6785 189 A F A IY Y I P L I 10 6786 203 V H R F G K Q A P A 10 6787 205 R F G K Q A P AY V 10 6788 208 K Q A P A Y V H T M 10 6789 237 K T K Q I R R A V I 106790 8 L S A T D L G L S I 9 6791 10 A T D L G L S I S T 9 6792 17 I S TL V T M L S I 9 6793 39 C L S H M F F I K F 9 6794 43 M F F I K F F T VM 9 6795 51 V M E S S V L L A M 9 6796 52 M E S S V L L A M A 9 6797 80D S R I A Q I G V A 9 6798 93 R G L L M L T P M V 9 6799 97 M L T P M VA L L I 9 6800 117 H H S Y C Y H P D V 9 6801 125 D V M K L S C T D T 96802 135 R I N S A V G L T A 9 6803 137 N S A V G L T A M F 9 6804 139 AV G L T A M F S T 9 6805 155 L I L L S Y V L I I 9 6806 161 V L I I R TV L S V 9 6807 181 S T C V S H I V A F 9 6808 182 T C V S H I V A F A 96809 183 C V S H I V A F A I 9 6810 193 Y Y I P L I S L S I 9 6811 197 LI S L S I V H R F 9 6812 207 G K Q A P A Y V H T 9 6813 212 A Y V H T MI A N T 9 6814 216 T M I A N T Y L L I 9 6815 236 V K T K Q I R R A V 96816 1 M Y Y F L S M L S A 8 6817 12 D L G L S I S T L V 8 6818 36 F N AC L S H M F F 8 6819 41 S H M F F I K F F T 8 6820 56 V L L A M A F D RF 8 6821 57 L L A M A F D R F V 8 6822 68 V S N P L R Y A M I 8 6823 75A M I L T D S R I A 8 6824 77 I L T D S R I A Q I 8 6825 79 T D S R I AQ I G V 8 6826 83 I A Q I G V A S V I 8 6827 131 C T D T R I N S A V 86828 154 L L I L L S Y V L I 8 6829 157 L L S Y V L I I R T 8 6830 171 AS P E E R K E T F 8 6831 175 E R K E T F S T C V 8 6832 178 E T F S T CV S H I 8 6833 179 T F S T C V S H I V 8 6834 209 Q A P A Y V H T M I 86835 229 M N P V I Y S V K T 8 6836 239 K Q I R R A V I K I 8 6837 2 Y YF L S M L S A T 7 6838 25 S I F W F N V R E I 7 6839 34 I S F N A C L SH M 7 6840 35 S F N A C L S H M F 7 6841 37 N A C L S H M F F I 7 684240 L S H M F F I K F F 7 6843 42 H M F F I K F F T V 7 6844 47 K F F T VM E S S V 7 6845 74 Y A M I L T D S R I 7 6846 94 G L L M L T P M V A 76847 106 I R L S Y C H S Q V 7 6848 118 H S Y C Y H P D V M 7 6849 127 MK L S C T D T R I 7 6850 134 T R I N S A V G L T 7 6851 140 V G L T A MF S T V 7 6852 162 L I I R T V L S V A 7 6853 173 P E E R K E T F S T 76854 180 F S T C V S H I V A 7 6855 186 H I V A F A I Y Y I 7 6856 220 NT Y L L I S P L M 7 6857 223 L L I S P L M N P V 7 6858 227 P L M N P VI Y S V 7 6859 232 V I Y S V K T K Q I 7 6860 18 S T L V T M L S I F 66861 20 L V T M L S I F W F 6 6862 22 T M L S I F W F N V 6 6863 27 F WF N V R E I S F 6 6864 29 F N V R E I S F N A 6 6865 66 V A V S N P L RY A 6 6866 84 A Q I G V A S V I R 6 6867 90 S V I R G L L M L T 6 686891 V I R G L L M L T P 6 6869 130 S C T D T R I N S A 6 6870 152 D L L LI L L S Y V 6 6871 158 L S Y V L I I R T V 6 6872 163 I I R T V L S V AS 6 6873 194 Y I P L I S L S I V 6 6874 201 S I V H R F G K Q A 6 6875235 S V K T K Q I R R A 6 6876 245 V I K I L H S K E T 6 6877 33 E I S FN A C L S H 5 6878 61 A F D R F V A V S N 5 6879 174 E E R K E T F S T C5 6880 23 M L S I F W F N V R 4 6881 30 N V R E I S F N A C 4 6882 44 FF I K F F T V M E 4 6883 71 P L R Y A M I L T D 4 6884 81 S R I A Q I GV A S 4 6885 101 M V A L L I R L S Y 4 6886 128 K L S C T D T R I N 46887 204 H R F G K Q A P A Y 4 6888 241 I R R A V I K I L H 4 6889 242 RR A V I K I L H S 4 6890 7 M L S A T D L G L S 3 6891 16 S I S T L V T ML S 3 6892 21 V T M L S I F W F N 3 6893 38 A C L S H M F F I K 3 689460 M A F D R F V A V S 3 6895 62 F D R F V A V S N P 3 6896 64 R F V A VS N P L R 3 6897 65 F V A V S N P L R Y 3 6898 73 R Y A M I L T D S R 36899 109 S Y C H S Q V L H H 3 6900 138 S A V G L T A M F S 3 6901 141 GL T A M F S T V G 3 6902 143 T A M F S T V G V D 3 6903 150 G V D L L LI L L S 3 6904 160 Y V L I I R T V L S 3 6905 164 I R T V L S V A S P 36906 176 R K E T F S T C V S 3 6907 177 K E T F S T C V S H 3 6908 199 SL S I V H R F G K 3 6909 217 M I A N T Y L L I S 3 6910 225 I S P L M NP V I Y 3 6911 233 I Y S V K T K Q I R 3 6912 244 A V I K I L H S K E 36913 5 L S M L S A T D L G 2 6914 24 L S I F W F N V R E 2 6915 26 I F WF N V R E I S 2 6916 54 S S V L L A M A F D 2 6917 72 L R Y A M I L T DS 2 6918 76 M I L T D S R I A Q 2 6919 85 Q I G V A S V I R G 2 6920 98L T P M V A L L I R 2 6921 103 A L L I R L S Y C H 2 6922 105 L I R L SY C H S Q 2 6923 108 L S Y C H S Q V L H 2 6924 111 C H S Q V L H H S Y2 6925 119 S Y C Y H P D V M K 2 6926 122 Y H P D V M K L S C 2 6927 132T D T R I N S A V G 2 6928 151 V D L L L I L L S Y 2 6929 165 R T V L SV A S P E 2 6930 167 V L S V A S P E E R 2 6931 184 V S H I V A F A I Y2 6932 187 I V A F A I Y Y I P 2 6933 190 F A I Y Y I P L I S 2 6934 196P L I S L S I V H R 2 6935 198 I S L S I V H R F G 2 6936 202 I V H R FG K Q A P 2 6937 221 T Y L L I S P L M N 2 6938 228 L M N P V I Y S V K2 6939 238 T K Q I R R A V I K 2 6940 3 Y F L S M L S A T D 1 6941 19 TL V T M L S I F W 1 6942 28 W F N V R E I S F N 1 6943 32 R E I S F N AC L S 1 6944 45 F I K F F T V M E S 1 6945 46 I K F F T V M E S S 1 694678 L T D S R I A Q I G 1 6947 100 P M V A L L I R L S 1 6948 116 L H H SY C Y H P D 1 6949 121 C Y H P D V M K L S 1 6950 126 V M K L S C T D TR 1 6951 129 L S C T D T R I N S 1 6952 156 I L L S Y V L I I R 1 6953166 T V L S V A S P E E 1 6954 168 L S V A S P E E R K 1 6955 169 S V AS P E E R K E 1 6956 192 I Y Y I P L I S L S 1 6957 200 L S I V H R F GK Q 1 6958 206 F G K Q A P A Y V H 1 6959 211 P A Y V H T M I A N 1 6960218 I A N T Y L L I S P 1 6961 231 P V I Y S V K T K Q 1 6962 234 Y S VK T K Q I R R 1 6963 243 R A V I K I L H S K 1 6964 HLA-B*4402 10-mersv.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 181 S T C V S H I V AF 17 6965 11 T D L G L S I S T L 16 6966 53 E S S V L L A M A F 16 6967144 A M F S T V G V D L 16 6968 185 S H I V A F A I Y Y 16 6969 204 H RF G K Q A P A Y 16 6970 219 A N T Y L L I S P L 16 6971 239 K Q I R R AV I K I 16 6972 240 Q I R R A V I K I L 16 6973 32 R E I S F N A C L S15 6974 40 L S H M F F I K F F 15 6975 89 A S V I R G L L M L 15 6976 95L L M L T P M V A L 15 6977 171 A S P E E R K E T F 15 6978 189 A F A IY Y I P L I 15 6979 191 A I Y Y I P L I S L 15 6980 193 Y Y I P L I S LS I 15 6981 15 L S I S T L V T M L 14 6982 27 F W F N V R E I S F 146983 39 C L S H M F F I K F 14 6984 69 S N P L R Y A M I L 14 6985 86 IG V A S V I R G L 14 6986 96 L M L T P M V A L L 14 6987 97 M L T P M VA L L I 14 6988 145 M F S T V G V D L L 14 6989 149 V G V D L L L I L L14 6990 151 V D L L L I L L S Y 14 6991 154 L L I L L S Y V L I 14 6992159 S Y V L I I R T V L 14 6993 174 E E R K E T F S T C 14 6994 197 L IS L S I V H R F 14 6995 213 Y V H T M I A N T Y 14 6996 225 I S P L M NP V I Y 14 6997 6 S M L S A T D L G L 13 6998 18 S T L V T M L S I F 136999 20 L V T M L S I F W F 13 7000 25 S I F W F N V R E I 13 7001 63 DR F V A V S N P L 13 7002 77 I L T D S R I A Q I 13 7003 99 T P M V A LL I R L 13 7004 101 M V A L L I R L S Y 13 7005 147 S T V G V D L L L I13 7006 178 E T F S T C V S H I 13 7007 188 V A F A I Y Y I P L 13 7008215 H T M I A N T Y L L 13 7009 216 T M I A N T Y L L I 13 7010 224 L IS P L M N P V I 13 7011 4 F L S M L S A T D L 12 7012 19 T L V T M L S IF W 12 7013 35 S F N A C L S H M F 12 7014 49 F T V M E S S V L L 127015 52 M E S S V L L A M A 12 7016 56 V L L A M A F D R F 12 7017 65 FV A V S N P L R Y 12 7018 87 G V A S V I R G L L 12 7019 107 R L S Y C HS Q V L 12 7020 111 C H S Q V L H H S Y 12 7021 113 S Q V L H H S Y C Y12 7022 120 Y C Y H P D V M K L 12 7023 133 D T R I N S A V G L 12 7024137 N S A V G L T A M F 12 7025 146 F S T V G V D L L L 12 7026 148 T VG V D L L L I L 12 7027 153 L L L I L L S Y V L 12 7028 155 L I L L S YV L I I 12 7029 173 P E E R K E T F S T 12 7030 177 K E T F S T C V S H12 7031 183 C V S H I V A F A I 12 7032 232 V I Y S V K T K Q I 12 703348 F F T V M E S S V L 11 7034 68 V S N P L R Y A M I 11 7035 184 V S HI V A F A I Y 11 7036 186 H I V A F A I Y Y I 11 7037 237 K T K Q I R RA V I 11 7038 8 L S A T D L G L S I 10 7039 17 I S T L V T M L S I 107040 31 V R E I S F N A C L 10 7041 36 F N A C L S H M F F 10 7042 37 NA C L S H M F F I 10 7043 83 I A Q I G V A S V I 10 7044 214 V H T M I AN T Y L 10 7045 74 Y A M I L T D S R I 9 7046 127 M K L S C T D T R I 97047 209 Q A P A Y V H T M I 9 7048 67 A V S N P L R Y A M 8 7049 75 A MI L T D S R I A 8 7050 84 A Q I G V A S V I R 8 7051 59 A M A F D R F VA V 7 7052 61 A F D R F V A V S N 7 7053 81 S R I A Q I G V A S 7 705490 S V I R G L L M L T 7 7055 150 G V D L L L I L L S 7 7056 170 V A S PE E R K E T 7 7057 196 P L I S L S I V H R 7 7058 208 K Q A P A Y V H TM 7 7059 244 A V I K I L H S K E 7 7060 2 Y Y F L S M L S A T 6 7061 10A T D L G L S I S T 6 7062 76 M I L T D S R I A Q 6 7063 121 C Y H P D VM K L S 6 7064 130 S C T D T R I N S A 6 7065 134 T R I N S A V G L T 67066 162 L I I R T V L S V A 6 7067 212 A Y V H T M I A N T 6 7068 235 SV K T K Q I R R A 6 7069 16 S I S T L V T M L S 5 7070 30 N V R E I S FN A C 5 7071 38 A C L S H M F F I K 5 7072 44 F F I K F F T V M E 5 707360 M A F D R F V A V S 5 7074 70 N P L R Y A M I L T 5 7075 71 P L R Y AM I L T D 5 7076 100 P M V A L L I R L S 5 7077 157 L L S Y V L I I R T5 7078 158 L S Y V L I I R T V 5 7079 161 V L I I R T V L S V 5 7080 190F A I Y Y I P L I S 5 7081 200 L S I V H R F G K Q 5 7082 227 P L M N PV I Y S V 5 7083 230 N P V I Y S V K T K 5 7084 5 L S M L S A T D L G 47085 13 L G L S I S T L V T 4 7086 14 G L S I S T L V T M 4 7087 23 M LS I F W F N V R 4 7088 24 L S I F W F N V R E 4 7089 33 E I S F N A C LS H 4 7090 34 I S F N A C L S H M 4 7091 42 H M F F I K F F T V 4 709243 M F F I K F F T V M 4 7093 47 K F F T V M E S S V 4 7094 50 T V M E SS V L L A 4 7095 51 V M E S S V L L A M 4 7096 55 S V L L A M A F D R 47097 80 D S R I A Q I G V A 4 7098 103 A L L I R L S Y C H 4 7099 104 LL I R L S Y C H S 4 7100 128 K L S C T D T R I N 4 7101 131 C T D T R IN S A V 4 7102 136 I N S A V G L T A M 4 7103 139 A V G L T A M F S T 47104 140 V G L T A M F S T V 4 7105 160 Y V L I I R T V L S 4 7106 163 II R T V L S V A S 4 7107 192 I Y Y I P L I S L S 4 7108 201 S I V H R FG K Q A 4 7109 210 A P A Y V H T M I A 4 7110 221 T Y L L I S P L M N 47111 223 L L I S P L M N P V 4 7112 226 S P L M N P V I Y S 4 7113 228 LM N P V I Y S V K 4 7114 231 P V I Y S V K T K Q 4 7115 236 V K T K Q IR R A V 4 7116 242 R R A V I K I L H S 4 7117 7 M L S A T D L G L S 37118 9 S A T D L G L S I S 3 7119 21 V T M L S I F W F N 3 7120 28 W F NV R E I S F N 3 7121 58 L A M A F D R F V A 3 7122 79 T D S R I A Q I GV 3 7123 88 V A S V I R G L L M 3 7124 91 V I R G L L M L T P 3 7125 93R G L L M L T P M V 3 7126 94 G L L M L T P M V A 3 7127 98 L T P M V AL L I R 3 7128 102 V A L L I R L S Y C 3 7129 109 S Y C H S Q V L H H 37130 122 Y H P D V M K L S C 3 7131 126 V M K L S C T D T R 3 7132 129 LS C T D T R I N S 3 7133 138 S A V G L T A M F S 3 7134 143 T A M F S TV G V D 3 7135 152 D L L L I L L S Y V 3 7136 156 I L L S Y V L I I R 37137 169 S V A S P E E R K E 3 7138 176 R K E T F S T C V S 3 7139 179 TF S T C V S H I V 3 7140 194 Y I P L I S L S I V 3 7141 195 I P L I S LS I V H 3 7142 199 S L S I V H R F G K 3 7143 202 I V H R F G K Q A P 37144 211 P A Y V H T M I A N 3 7145 217 M I A N T Y L L I S 3 7146 218 IA N T Y L L I S P 3 7147 220 N T Y L L I S P L M 3 7148 229 M N P V I YS V K T 3 7149 3 Y F L S M L S A T D 2 7150 12 D L G L S I S T L V 27151 41 S H M F F I K F F T 2 7152 46 I K F F T V M E S S 2 7153 54 S SV L L A M A F D 2 7154 66 V A V S N P L R Y A 2 7155 78 L T D S R I A QI G 2 7156 85 Q I G V A S V I R G 2 7157 92 I R G L L M L T P M 2 7158105 L I R L S Y C H S Q 2 7159 106 I R L S Y C H S Q V 2 7160 108 L S YC H S Q V L H 2 7161 110 Y C H S Q V L H H S 2 7162 118 H S Y C Y H P DV M 2 7163 119 S Y C Y H P D V M K 2 7164 123 H P D V M K L S C T 2 7165132 T D T R I N S A V G 2 7166 135 R I N S A V G L T A 2 7167 142 L T AM F S T V G V 2 7168 165 R T V L S V A S P E 2 7169 167 V L S V A S P EE R 2 7170 175 E R K E T F S T C V 2 7171 180 F S T C V S H I V A 2 7172198 I S L S I V H R F G 2 7173 206 F G K Q A P A Y V H 2 7174 222 Y L LI S P L M N P 2 7175 238 T K Q I R R A V I K 2 7176 241 I R R A V I K IL H 2 7177 243 R A V I K I L H S K 2 7178 245 V I K I L H S K E T 2 71791 M Y Y F L S M L S A 1 7180 22 T M L S I F W F N V 1 7181 26 I F W F NV R E I S 1 7182 29 F N V R E I S F N A 1 7183 45 F I K F F T V M E S 17184 57 L L A M A F D R F V 1 7185 62 F D R F V A V S N P 1 7186 64 R FV A V S N P L R 1 7187 72 L R Y A M I L T D S 1 7188 73 R Y A M I L T DS R 1 7189 82 R I A Q I G V A S V 1 7190 114 Q V L H H S Y C Y H 1 7191116 L H H S Y C Y H P D 1 7192 117 H H S Y C Y H P D V 1 7193 124 P D VM K L S C T D 7194 HLA-A*0201 10-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 89 0 score SEQ ID 58 S L H E P M Y Y F L 25 7195 8 N I T S T S I I F L 217196 43 L L G N S L I L F A 21 7197 5 T L Q N I T S T S I 20 7198 9 I TS T S I I F L L 20 7199 15 I F L L T G V P G L 20 7200 17 L L T G V P GL E A 20 7201 42 A L L G N S L I L F 20 7202 31 I S I P F C F L S V 197203 39 S V T A L L G N S L 18 7204 12 T S I I F L L T G V 17 7205 32 SI P F C F L S V T 17 7206 37 F L S V T A L L G N 17 7207 41 T A L L G NS L I L 17 7208 50 L F A T I T Q P S L 17 7209 47 S L I L F A T I T Q 167210 40 V T A L L G N S L I 15 7211 48 L I L F A T I T Q P 15 7212 35 FC F L S V T A L L 14 7213 53 T I T Q P S L H E P 14 7214 1 F I T S T L QN I T 13 7215 11 S T S I I F L L T G 13 7216 14 I I F L L T G V P G 137217 16 F L L T G V P G L E 13 7218 24 L E A F H T W I S I 13 7219 45 GN S L I L F A T I 13 7220 49 I L F A T I T Q P S 13 7221 29 T W I S I PF C F L 12 7222 44 L G N S L I L F A T 12 7223 54 I T Q P S L H E P M 127224 6 L Q N I T S T S I I 11 7225 13 S I I F L L T G V P 11 7226 18 L TG V P G L E A F 11 7227 20 G V P G L E A F H T 11 7228 33 I P F C F L SV T A 11 7229 34 P F C F L S V T A L 11 7230 61 E P M Y Y F L S M L 117231 4 S T L Q N I T S T S 10 7232 23 G L E A F H T W I S 10 7233 3 T ST L Q N I T S T 9 7234 22 P G L E A F H T W I 9 7235 52 A T I T Q P S LH E 9 7236 2 I T S T L Q N I T S 8 7237 30 W I S I P F C F L S 8 7238 60H E P M Y Y F L S M 7 7239 25 E A F H T W I S I P 6 7240 38 L S V T A LL G N S 6 7241 46 N S L I L F A T I T 6 7242 27 F H T W I S I P F C 57243 28 H T W I S I P F C F 5 7244 62 P M Y Y F L S M L S 5 7245 10 T ST S I I F L L T 4 7246 19 T G V P G L E A F H 4 7247 21 V P G L E A F HT W 4 7248 51 F A T I T Q P S L H 4 7249 36 C F L S V T A L L G 3 725059 L H E P M Y Y F L S 3 7251 7 Q N I T S T S I I F 2 7252 26 A F H T WI S I P F 2 7253 55 T Q P S L H E P M Y 1 7254 HLA-A*0202 10-mers v.1B:238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 24 L E A F H T W I S I 37255 40 V T A L L G N S L I 3 7256 50 L F A T I T Q P S L 3 7257 25 E AF H T W I S I P 2 7258 41 T A L L G N S L I L 2 7259 51 F A T I T Q P SL H 2 7260 26 A F H T W I S I P F 1 7261 42 A L L G N S L I L F 1 726252 A T I T Q P S L H E 1 7263 HLA-A*0203 10-mers v.1B: 238P1B2 Pos 1 2 34 5 6 7 8 9 0 score SEQ ID 17 L L T G V P G L E A 10 7264 33 I P F C F LS V T A 10 7265 43 L L G N S L I L F A 10 7266 18 L T G V P G L E A F 97267 34 P F C F L S V T A L 9 7268 44 L G N S L I L F A T 9 7269 19 T GV P G L E A F H 8 7270 35 F C F L S V T A L L 8 7271 45 G N S L I L F AT I 8 7272 HLA-A1 10-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 scoreSEQ ID 31 I S I P F C F L S V 17 7273 55 T Q P S L H E P M Y 16 7274 59L H E P M Y Y F L S 16 7275 10 T S T S I I F L L T 15 7276 56 Q P S L HE P M Y Y 15 7277 11 S T S I I F L L T G 14 7278 52 A T I T Q P S L H E13 7279 2 I T S T L Q N I T S 11 7280 23 G L E A F H T W I S 11 7281 40V T A L L G N S L I 10 7282 54 I T Q P S L H E P M 10 7283 17 L L T G VP G L E A 9 7284 42 A L L G N S L I L F 9 7285 60 H E P M Y Y F L S M 97286 4 S T L Q N I T S T S 8 7287 9 I T S T S I I F L L 8 7288 36 C F LS V T A L L G 8 7289 37 F L S V T A L L G N 8 7290 43 L L G N S L I L FA 7 7291 47 S L I L F A T I T Q 7 7292 18 L T G V P G L E A F 6 7293 28H T W I S I P F C F 6 7294 41 T A L L G N S L I L 6 7295 26 A F H T W IS I P F 5 7296 3 T S T L Q N I T S T 4 7297 7 Q N I T S T S I I F 4 72988 N I T S T S I I F L 4 7299 12 T S I I F L L T G V 4 7300 16 F L L T GV P G L E 4 7301 19 T G V P G L E A F H 4 7302 21 V P G L E A F H T W 47303 24 L E A F H T W I S I 4 7304 38 L S V T A L L G N S 4 7305 46 N SL I L F A T I T 4 7306 57 P S L H E P M Y Y F 4 7307 13 S I I F L L T GV P 3 7308 29 T W I S I P F C F L 3 7309 32 S I P F C F L S V T 3 731035 F C F L S V T A L L 3 7311 39 S V T A L L G N S L 3 7312 45 G N S L IL F A T I 3 7313 51 F A T I T Q P S L H 3 7314 58 S L H E P M Y Y F L 37315 30 W I S I P F C F L S 2 7316 62 P M Y Y F L S M L S 2 7317 1 F I TS T L Q N I T 1 7318 5 T L Q N I T S T S I 1 7319 14 I I F L L T G V P G1 7320 15 I F L L T G V P G L 1 7321 20 G V P G L E A F H T 1 7322 27 FH T W I S I P F C 1 7323 34 P F C F L S V T A L 1 7324 49 I L F A T I TQ P S 1 7325 61 E P M Y Y F L S M L 1 7326 HLA-A26 10-mers v.1B: 238P1B2Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 18 L T G V P G L E A F 25 7327 42 AL L G N S L I L F 24 7328 8 N I T S T S I I F L 23 7329 9 I T S T S I IF L L 22 7330 58 S L H E P M Y Y F L 22 7331 15 I F L L T G V P G L 207332 28 H T W I S I P F C F 20 7333 54 I T Q P S L H E P M 20 7334 61 EP M Y Y F L S M L 20 7335 34 P F C F L S V T A L 19 7336 39 S V T A L LG N S L 19 7337 50 L F A T I T Q P S L 17 7338 26 A F H T W I S I P F 167339 32 S I P F C F L S V T 16 7340 53 T I T Q P S L H E P 16 7341 29 TW I S I P F C F L 15 7342 48 L I L F A T I T Q P 15 7343 11 S T S I I FL L T G 14 7344 20 G V P G L E A F H T 14 7345 55 T Q P S L H E P M Y 147346 57 P S L H E P M Y Y F 14 7347 60 H E P M Y Y F L S M 14 7348 14 II F L L T G V P G 13 7349 25 E A F H T W I S I P 13 7350 37 F L S V T AL L G N 13 7351 52 A T I T Q P S L H E 13 7352 4 S T L Q N I T S T S 127353 7 Q N I T S T S I I F 12 7354 13 S I I F L L T G V P 12 7355 40 V TA L L G N S L I 12 7356 43 L L G N S L I L F A 12 7357 1 F I T S T L Q NI T 11 7358 17 L L T G V P G L E A 11 7359 35 F C F L S V T A L L 117360 49 I L F A T I T Q P S 11 7361 56 Q P S L H E P M Y Y 11 7362 2 I TS T L Q N I T S 10 7363 30 W I S I P F C F L S 10 7364 47 S L I L F A TI T Q 10 7365 5 T L Q N I T S T S I 9 7366 31 I S I P F C F L S V 9 736716 F L L T G V P G L E 8 7368 23 G L E A F H T W I S 8 7369 41 T A L L GN S L I L 8 7370 12 T S I I F L L T G V 7 7371 36 C F L S V T A L L G 77372 44 L G N S L I L F A T 6 7373 59 L H E P M Y Y F L S 6 7374 3 T S TL Q N I T S T 5 7375 10 T S T S I I F L L T 5 7376 27 F H T W I S I P FC 5 7377 38 L S V T A L L G N S 5 7378 45 G N S L I L F A T I 5 8903 21V P G L E A F H T W 4 8904 19 T G V P G L E A F H 3 8905 33 I P F C F LS V T A 3 8906 22 P G L E A F H T W I 2 8907 24 L E A F H T W I S I 28908 6 L Q N I T S T S I I 1 8909 51 F A T I T Q P S L H 1 8910 62 P M YY F L S M L S 1 8911 HLA-A3 10-mers v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 90 score SEQ ID 42 A L L G N S L I L F 21 7379 47 S L I L F A T I T Q 197380 14 I I F L L T G V P G 18 7381 17 L L T G V P G L E A 18 7382 39 SV T A L L G N S L 18 7383 13 S I I F L L T G V P 17 7384 32 S I P F C FL S V T 16 7385 20 G V P G L E A F H T 15 7386 5 T L Q N I T S T S I 147387 16 F L L T G V P G L E 14 7388 43 L L G N S L I L F A 14 7389 48 LI L F A T I T Q P 14 7390 49 I L F A T I T Q P S 14 7391 31 I S I P F CF L S V 13 7392 37 F L S V T A L L G N 13 7393 23 G L E A F H T W I S 127394 58 S L H E P M Y Y F L 12 7395 56 Q P S L H E P M Y Y 11 7396 4 S TL Q N I T S T S 10 7397 19 T G V P G L E A F H 10 7398 33 I P F C F L SV T A 10 7399 7 Q N I T S T S I I F 9 7400 11 S T S I I F L L T G 9 740130 W I S I P F C F L S 9 7402 51 F A T I T Q P S L H 9 7403 52 A T I T QP S L H E 9 7404 1 F I T S T L Q N I T 8 7405 8 N I T S T S I I F L 87406 36 C F L S V T A L L G 8 7407 45 G N S L I L F A T I 8 7408 53 T IT Q P S L H E P 8 7409 26 A F H T W I S I P F 7 7410 46 N S L I L F A TI T 7 7411 55 T Q P S L H E P M Y 7 7412 2 I T S T L Q N I T S 6 7413 28H T W I S I P F C F 6 7414 41 T A L L G N S L I L 6 7415 57 P S L H E PM Y Y F 6 7416 12 T S I I F L L T G V 5 7417 15 I F L L T G V P G L 57418 18 L T G V P G L E A F 5 7419 21 V P G L E A F H T W 5 7420 22 P GL E A F H T W I 5 7421 40 V T A L L G N S L I 5 7422 54 I T Q P S L H EP M 5 7423 60 H E P M Y Y F L S M 5 7424 62 P M Y Y F L S M L S 5 7425 3T S T L Q N I T S T 4 7426 6 L Q N I T S T S I I 4 7427 35 F C F L S V TA L L 4 7428 61 E P M Y Y F L S M L 4 7429 10 T S T S I I F L L T 3 743024 L E A F H T W I S I 3 7431 25 E A F H T W I S I P 3 7432 29 T W I S IP F C F L 3 7433 50 L F A T I T Q P S L 3 7434 59 L H E P M Y Y F L S 37435 9 I T S T S I I F L L 2 7436 34 P F C F L S V T A L 2 7437 38 L S VT A L L G N S 1 7438 44 L G N S L I L F A T 1 7439 HLA-B*0702 10-mersv.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 61 E P M Y Y F L S ML 22 7440 33 I P F C F L S V T A 19 7441 9 I T S T S I I F L L 13 744215 I F L L T G V P G L 13 7443 34 P F C F L S V T A L 13 7444 21 V P G LE A F H T W 12 7445 29 T W I S I P F C F L 12 7446 35 F C F L S V T A LL 12 7447 41 T A L L G N S L I L 12 7448 50 L F A T I T Q P S L 12 744956 Q P S L H E P M Y Y 12 7450 8 N I T S T S I I F L 11 7451 31 I S I PF C F L S V 11 7452 39 S V T A L L G N S L 11 7453 58 S L H E P M Y Y FL 11 7454 17 L L T G V P G L E A 10 7455 42 A L L G N S L I L F 10 745643 L L G N S L I L F A 10 7457 45 G N S L I L F A T I 10 7458 10 T S T SI I F L L T 9 7459 26 A F H T W I S I P F 9 7460 54 I T Q P S L H E P M9 7461 60 H E P M Y Y F L S M 9 7462 18 L T G V P G L E A F 8 7463 20 GV P G L E A F H T 8 7464 3 T S T L Q N I T S T 7 7465 5 T L Q N I T S TS I 7 7466 6 L Q N I T S T S I I 7 7467 12 T S I I F L L T G V 7 7468 22P G L E A F H T W I 7 7469 24 L E A F H T W I S I 7 7470 32 S I P F C FL S V T 7 7471 40 V T A L L G N S L I 7 7472 44 L G N S L I L F A T 77473 46 N S L I L F A T I T 7 7474 1 F I T S T L Q N I T 6 7475 7 Q N IT S T S I I F 6 7476 28 H T W I S I P F C F 6 7477 57 P S L H E P M Y YF 6 7478 11 S T S I I F L L T G 4 7479 14 I I F L L T G V P G 4 7480 37F L S V T A L L G N 4 7481 49 I L F A T I T Q P S 4 7482 52 A T I T Q PS L H E 4 7483 2 I T S T L Q N I T S 3 7484 19 T G V P G L E A F H 37485 13 S I I F L L T G V P 2 7486 23 G L E A F H T W I S 2 7487 27 F HT W I S I P F C 2 7488 30 W I S I P F C F L S 2 7489 36 C F L S V T A LL G 2 7490 4 S T L Q N I T S T S 1 7491 25 E A F H T W I S I P 1 7492 47S L I L F A T I T Q 1 7493 48 L I L F A T I I Q P 1 7494 55 T Q P S L HE P M Y 1 7495 59 L H E P M Y Y F L S 1 7496 HLA-B*4402 10-mers v.1B:238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 24 L E A F H T W I S I 197497 42 A L L G N S L I L F 18 7498 9 I T S T S I I F L L 16 7499 7 Q NI T S T S I I F 15 7500 8 N I T S T S I I F L 15 7501 26 A F H T W I S IP F 15 7502 35 F C F L S V T A L L 15 7503 21 V P G L E A F H T W 147504 29 T W I S I P F C F L 14 7505 61 E P M Y Y F L S M L 14 7506 15 IF L L T G V P G L 13 7507 18 L T G V P G L E A F 13 7508 34 P F C F L SV T A L 13 7509 41 T A L L G N S L I L 13 7510 56 Q P S L H E P M Y Y 137511 60 H E P M Y Y F L S M 13 7512 39 S V T A L L G N S L 12 7513 45 GN S L I L F A T I 12 7514 28 H T W I S I P F C F 11 7515 50 L F A T I TQ P S L 11 7516 55 T Q P S L H E P M Y 11 7517 57 P S L H E P M Y Y F 117518 58 S L H E P M Y Y F L 11 7519 40 V T A L L G N S L I 10 7520 5 T LQ N I T S T S I 9 7521 6 L Q N I T S T S I I 9 7522 22 P G L E A F H T WI 9 7523 31 I S I P F C F L S V 8 7524 47 S L I L F A T I T Q 8 7525 52A T I T Q P S L H E 8 7526 25 E A F H T W I S I P 7 7527 13 S I I F L LT G V P 6 7528 11 S T S I I F L L T G 5 7529 43 L L G N S L I L F A 57530 48 L I L F A T I T Q P 5 7531 2 I T S T L Q N I T S 4 7532 3 T S TL Q N I T S T 4 7533 4 S T L Q N I T S T S 4 7534 12 T S I I F L L T G V4 7535 14 I I F L L T G V P G 4 7536 16 F L L T G V P G L E 4 7537 32 SI P F C F L S V T 4 7538 33 I P F C F L S V T A 4 7539 36 C F L S V T AL L G 4 7540 59 L H E P M Y Y F L S 4 7541 10 T S T S I I F L L T 7542HLA-A*0201 10-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 8 LL T S P L M N P V 22 7543 7 Y L L T S P L M N P 18 7544 2 M I A N T Y LL T S 17 7545 9 L T S P L M N P V I 17 7546 1 T M I A N T Y L L T 157547 3 I A N T Y L L T S P 13 7548 4 A N T Y L L T S P L 10 7549 5 N T YL L T S P L M 10 7550 6 T Y L L T S P L M N 3 7551 10 T S P L M N P V IY 2 7552 HLA-A*0202 10-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 scoreSEQ ID 2 M I A N T Y L L T S 3 7553 3 I A N T Y L L T S P 2 7554 4 A N TY L L T S P L 1 7555 HLA-A1 10-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0score SEQ ID 10 T S P L M N P V I Y 19 7556 9 L T S P L M N P V I 127557 1 T M I A N T Y L L T 8 7558 5 N T Y L L T S P L M 8 7559 6 T Y L LT S P L M N 7 7560 2 M I A N T Y L L T S 6 7561 7 Y L L T S P L M N P 37562 4 A N T Y L L T S P L 1 7563 8 L L T S P L M N P V 1 7564 HLA-A2610-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 5 N T Y L L TS P L M 19 7565 2 M I A N T Y L L T S 15 7566 7 Y L L T S P L M N P 147567 8 L L T S P L M N P V 13 7568 9 L T S P L M N P V I 13 7569 10 T SP L M N P V I Y 12 7570 4 A N T Y L L T S P L 9 7571 1 T M I A N T Y L LT 6 7572 3 I A N T Y L L T S P 5 7573 6 T Y L L T S P L M N 1 7574HLA-A3 10-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 2 M I AN T Y L L T S 17 7575 7 Y L L T S P L M N P 13 7576 10 T S P L M N P V IY 12 7577 8 L L T S P L M N P V 10 7578 1 T M I A N T Y L L T 8 7579 6 TY L L T S P L M N 8 7580 9 L T S P L M N P V I 7 7581 4 A N T Y L L T SP L 6 7582 3 I A N T Y L L T S P 5 7583 5 N T Y L L T S P L M 5 7584HLA-B*0702 10-mers v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 score SEQ ID 4 AN T Y L L T S P L 14 7585 9 L T S P L M N P V I 11 7586 1 T M I A N T YL L T 7587

TABLE XIXC part 1 HLA-DRB1*0101 15 - mers v.1: 238P1B2 Pos 1 2 3 4 5 6 78 9 0 1 2 3 4 5 score SEQ ID 2 Y Y F L S M L S A T D L G L S 34 7588 151V D L L L I L L S Y V L I I R 33 7589 46 I K F F T V M E S S V L L A M32 7590 191 A I Y Y I P L I S L S I V H R 32 7591 203 V H R F G K Q A PA Y V H T M 32 7592 92 I R G L L M L T P M V A L L I 31 7593 95 L L M LT P M V A L L I R L S 31 7594 158 L S Y V L I I R T V L S V A S 31 759514 G L S I S T L V T M L S I F W 30 7596 161 V L I I R T V L S V A S P EE 30 7597 181 S T C V S H I V A F A I Y Y I 30 7598 230 N P V I Y S V KT K Q I R R A 29 7599 157 L L S Y V L I I R T V L S V A 27 7600 18 S T LV T M L S I F W F N V R 26 7601 89 A S V I R G L L M L T P M V A 26 760298 L T P M V A L L I R L S Y C H 26 7603 199 S L S I V H R F G K Q A P AY 26 7604 33 E I S F N A C L S H M F F I K 25 7605 133 D T R I N S A V GL T A M F S 25 7606 136 I N S A V G L T A M F S T V G 25 7607 143 T A MF S T V G V D L L L I L 25 7608 148 T V G V D L L L I L L S Y V L 257609 152 D L L L I L L S Y V L I I R T 25 7610 10 A T D L G L S I S T LV T M L 24 7611 25 S I F W F N V R E I S F N A C 24 7612 45 F I K F F TV M E S S V L L A 24 7613 51 V M E S S V L L A M A F D R F 24 7614 73 RY A M I L T D S R I A Q I G 24 7615 102 V A L L I R L S Y C H S Q V L 247616 142 L T A M F S T V G V D L L L I 24 7617 177 K E T F S T C V S H IV A F A 24 7618 222 Y L L I S P L M N P V I Y S V 24 7619 37 N A C L S HM F F I K F F T V 23 7620 40 L S H M F F I K F F T V M E S 23 7621 71 PL R Y A M I L T D S R I A Q 23 7622 80 D S R I A Q I G V A S V I R G 237623 131 C T D T R I N S A V G L T A M 23 7624 150 G V D L L L I L L S YV L I I 23 7625 192 I Y Y I P L I S L S I V H R F 23 7626 218 I A N T YL L I S P L M N P V 23 7627 219 A N T Y L L I S P L M N P V I 23 7628 1M Y Y F L S M L S A T D L G L 22 7629 20 L V T M L S I F W F N V R E I22 7630 41 S H M F F I K F F T V M E S S 22 7631 54 S S V L L A M A F DR F V A V 22 7632 79 T D S R I A Q I G V A S V I R 22 7633 85 Q I G V AS V I R G L L M L T 22 7634 86 I G V A S V I R G L L M L T P 22 7635 105L I R L S Y C H S Q V L H H S 22 7636 139 A V G L T A M F S T V G V D L22 7637 189 A F A I Y Y I P L I S L S I V 22 7638 211 P A Y V H T M I AN T Y L L I 22 7639 17 I S T L V T M L S I F W F N V 21 7640 91 V I R GL L M L T P M V A L L 21 7641 187 I V A F A I Y Y I P L I S L S 21 7642190 F A I Y Y I P L I S L S I V H 21 7643 164 I R T V L S V A S P E E RK E 20 7644 208 K Q A P A Y V H T M I A N T Y 20 7645 12 D L G L S I S TL V T M L S I 19 7646 24 L S I F W F N V R E I S F N A 19 7647 72 L R YA M I L T D S R I A Q I 19 7648 81 S R I A Q I G V A S V I R G L 19 7649119 S Y C Y H P D V M K L S C T D 19 7650 123 H P D V M K L S C T D T RI N 19 7651 159 S Y V L I I R T V L S V A S P 19 7652 197 L I S L S I VH R F G K Q A P 19 7653 220 N T Y L L I S P L M N P V I Y 19 7654 238 TK Q I R R A V I K I L H S K 19 7655 4 F L S M L S A T D L G L S I S 187656 7 M L S A T D L G L S I S T L V 18 7657 42 H M F F I K F F T V M ES S V 18 7658 43 M F F I K F F T V M E S S V L 18 7659 55 S V L L A M AF D R F V A V S 18 7660 59 A M A F D R F V A V S N P L R 18 7661 90 S VI R G L L M L T P M V A L 18 7662 233 I Y S V K T K Q I R R A V I K 187663 234 Y S V K T K Q I R R A V I K I 18 7664 23 M L S I F W F N V R EI S F N 17 7665 53 E S S V L L A M A F D R F V A 17 7666 57 L L A M A FD R F V A V S N P 17 7667 60 M A F D R F V A V S N P L R Y 17 7668 62 FD R F V A V S N P L R Y A M 17 7669 66 V A V S N P L R Y A M I L T D 177670 67 A V S N P L R Y A M I L T D S 17 7671 75 A M I L T D S R I A Q IG V A 17 7672 93 R G L L M L T P M V A L L I R 17 7673 99 T P M V A L LI R L S Y C H S 17 7674 101 M V A L L I R L S Y C H S Q V 17 7675 140 VG L T A M F S T V G V D L L 17 7676 147 S T V G V D L L L I L L S Y V 177677 153 L L L I L L S Y V L I I R T V 17 7678 156 I L L S Y V L I I R TV L S V 17 7679 162 L I I R T V L S V A S P E E R 17 7680 184 V S H I VA F A I Y Y I P L I 17 7681 185 S H I V A F A I Y Y I P L I S 17 7682195 I P L I S L S I V H R F G K Q 17 7683 200 L S I V H R F G K Q A P AY V 17 7684 212 A Y V H T M I A N T Y L L I S 17 7685 213 Y V H T M I AN T Y L L I S P 17 7686 217 M I A N T Y L L I S P L M N P 17 7687 5 L SM L S A T D L G L S I S T 16 7688 6 S M L S A T D L G L S I S T L 167689 9 S A T D L G L S I S T L V T M 16 7690 15 L S I S T L V T M L S IF W F 16 7691 28 W F N V R E I S F N A C L S H 16 7692 30 N V R E I S FN A C L S H M F 16 7693 34 I S F N A C L S H M F F I K F 16 7694 47 K FF T V M E S S V L L A M A 16 7695 48 F F T V M E S S V L L A M A F 167696 49 F T V M E S S V L L A M A F D 16 7697 65 F V A V S N P L R Y A MI L T 16 7698 77 I L T D S R I A Q I G V A S V 16 7699 94 G L L M L T PM V A L L I R L 16 7700 113 S Q V L H H S Y C Y H P D V M 16 7701 124 PD V M K L S C T D T R I N S 16 7702 134 T R I N S A V G L T A M F S T 167703 146 F S T V G V D L L L I L L S Y 16 7704 160 Y V L I I R T V L S VA S P E 16 7705 173 P E E R K E T F S T C V S H I 16 7706 194 Y I P L IS L S I V H R F G K 16 7707 214 V H T M I A N T Y L L I S P L 16 7708215 H T M I A N T Y L L I S P L M 16 7709 221 T Y L L I S P L M N P V IY S 16 7710 225 I S P L M N P V I Y S V K T K 16 7711 27 F W F N V R E IS F N A C L S 15 7712 70 N P L R Y A M I L T D S R I A 15 7713 126 V M KL S C T D T R I N S A V 15 7714 145 M F S T V G V D L L L I L L S 157715 178 E T F S T C V S H I V A F A I 15 7716 226 S P L M N P V I Y S VK T K Q 15 7717 235 S V K T K Q I R R A V I K I L 15 7718 50 T V M E S SV L L A M A F D R 14 7719 61 A F D R F V A V S N P L R Y A 14 7720 63 DR F V A V S N P L R Y A M I 14 7721 108 L S Y C H S Q V L H H S Y C Y 147722 116 L H H S Y C Y H P D V M K L S 14 7723 135 R I N S A V G L T A MF S T V 14 7724 155 L I L L S Y V L I I R T V L S 14 7725 165 R T V L SV A S P E E R K E T 14 7726 174 E E R K E T F S T C V S H I V 14 7727186 H I V A F A I Y Y I P L I S L 14 7728 188 V A F A I Y Y I P L I S LS I 14 7729 240 Q I R R A V I K I L H S K E T 14 7730 78 L T D S R I A QI G V A S V I 13 7731 87 G V A S V I R G L L M L T P M 13 7732 130 S C TD T R I N S A V G L T A 13 7733 223 L L I S P L M N P V I Y S V K 137734 227 P L M N P V I Y S V K T K Q I 13 7735 11 T D L G L S I S T L VT M L S 12 7736 26 I F W F N V R E I S F N A C L 12 7737 82 R I A Q I GV A S V I R G L L 12 7738 84 A Q I G V A S V I R G L L M L 12 7739 21 VT M L S I F W F N V R E I S 11 7740 29 F N V R E I S F N A C L S H M 117741 103 A L L I R L S Y C H S Q V L H 11 7742 167 V L S V A S P E E R KE T F S 11 7743 201 S I V H R F G K Q A P A Y V H 11 7744 210 A P A Y VH T M I A N T Y L L 11 7745 236 V K T K Q I R R A V I K I L H 11 7746 38A C L S H M F F I K F F T V M 10 7747 52 M E S S V L L A M A F D R F V10 7748 64 R F V A V S N P L R Y A M I L 10 7749 69 S N P L R Y A M I LT D S R I 10 7750 107 R L S Y C H S Q V L H H S Y C 10 7751 117 H H S YC Y H P D V M K L S C 10 7752 163 I I R T V L S V A S P E E R K 10 7753229 M N P V I Y S V K T K Q I R R 10 7754 231 P V I Y S V K T K Q I R RA V 10 7755 13 L G L S I S T L V T M L S I F 9 7756 31 V R E I S F N A CL S H M F F 9 7757 35 S F N A C L S H M F F I K F F 9 7758 44 F F I K FF T V M E S S V L L 9 7759 118 H S Y C Y H P D V M K L S C T 9 7760 125D V M K L S C T D T R I N S A 9 7761 128 K L S C T D T R I N S A V G L 97762 137 N S A V G L T A M F S T V G V 9 7763 144 A M F S T V G V D L LL I L L 9 7764 149 V G V D L L L I L L S Y V L I 9 7765 170 V A S P E ER K E T F S T C V 9 7766 180 F S T C V S H I V A F A I Y Y 9 7767 182 TC V S H I V A F A I Y Y I P 9 7768 193 Y Y I P L I S L S I V H R F G 97769 204 H R F G K Q A P A Y V H T M I 9 7770 207 G K Q A P A Y V H T MI A N T 9 7771 216 T M I A N T Y L L I S P L M N 9 7772 224 L I S P L MN P V I Y S V K T 9 7773 237 K T K Q I R R A V I K I L H S 9 7774 16 S IS T L V T M L S I F W F N 8 7775 32 R E I S F N A C L S H M F F I 8 777656 V L L A M A F D R F V A V S N 8 7777 58 L A M A F D R F V A V S N P L8 7778 74 Y A M I L T D S R I A Q I G V 8 7779 76 M I L T D S R I A Q IG V A S 8 7780 83 I A Q I G V A S V I R G L L M 8 7781 88 V A S V I R GL L M L T P M V 8 7782 97 M L T P M V A L L I R L S Y C 8 7783 104 L L IR L S Y C H S Q V L H H 8 7784 110 Y C H S Q V L H H S Y C Y H P 8 7785111 C H S Q V L H H S Y C Y H P D 8 7786 112 H S Q V L H H S Y C Y H P DV 8 7787 115 V L H H S Y C Y H P D V M K L 8 7788 122 Y H P D V M K L SC T D T R I 8 7789 127 M K L S C T D T R I N S A V G 8 7790 129 L S C TD T R I N S A V G L T 8 7791 138 S A V G L T A M F S T V G V D 8 7792154 L L I L L S Y V L I I R T V L 8 7793 169 S V A S P E E R K E T F S TC 8 7794 176 R K E T F S T C V S H I V A F 8 7795 179 T F S T C V S H IV A F A I Y 8 7796 183 C V S H I V A F A I Y Y I P L 8 7797 202 I V H RF G K Q A P A Y V H T 8 7798 206 F G K Q A P A Y V H T M I A N 8 7799239 K Q I R R A V I K I L H S K E 8 7800 3 Y F L S M L S A T D L G L S I7 7801 8 L S A T D L G L S I S T L V T 7 7802 96 L M L T P M V A L L I RL S Y 7 7803 100 P M V A L L I R L S Y C H S Q 7 7804 171 A S P E E R KE T F S T C V S 7 7805 196 P L I S L S I V H R F G K Q A 7 7806 109 S YC H S Q V L H H S Y C Y H 6 7807 120 Y C Y H P D V M K L S C T D T 67808 121 C Y H P D V M K L S C T D T R 6 7809 228 L M N P V I Y S V K TK Q I R 5 7810 172 S P E E R K E T F S T C V S H 4 7811 232 V I Y S V KT K Q I R R A V I 3 7812 168 L S V A S P E E R K E T F S T 2 7813 175 ER K E T F S T C V S H I V A 2 7814 19 T L V T M L S I F W F N V R E 17815 22 T M L S I F W F N V R E I S F 1 7816 39 C L S H M F F I K F F TV M E 1 7817 141 G L T A M F S T V G V D L L L 1 7818 166 T V L S V A SP E E R K E T F 1 7819 198 I S L S I V H R F G K Q A P A 1 7820HLA-DRB1*0301 (DR17) 15 - mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 23 4 5 score SEQ ID 74 Y A M I L T D S R I A Q I G V 30 7821 146 F S T VG V D L L L I L L S Y 30 7822 85 Q I G V A S V I R G L L M L T 26 782399 T P M V A L L I R L S Y C H S 26 7824 4 F L S M L S A T D L G L S I S22 7825 57 L L A M A F D R F V A V S N P 22 7826 93 R G L L M L T P M VA L L I R 22 7827 94 G L L M L T P M V A L L I R L 22 7828 18 S T L V TM L S I F W F N V R 21 7829 151 V D L L L I L L S Y V L I I R 21 7830 2Y Y F L S M L S A T D L G L S 20 7831 54 S S V L L A M A F D R F V A V20 7832 142 L T A M F S T V G V D L L L I 20 7833 37 N A C L S H M F F IK F F T V 19 7834 63 D R F V A V S N P L R Y A M I 19 7835 105 L I R L SY C H S Q V L H H S 19 7836 167 V L S V A S P E E R K E T F S 19 7837189 A F A I Y Y I P L I S L S I V 19 7838 195 I P L I S L S I V H R F GK Q 19 7839 200 L S I V H R F G K Q A P A Y V 19 7840 211 P A Y V H T MI A N T Y L L I 19 7841 238 T K Q I R R A V I K I L H S K 19 7842 46 I KF F T V M E S S V L L A M 18 7843 65 F V A V S N P L R Y A M I L T 187844 143 T A M F S T V G V D L L L I L 18 7845 229 M N P V I Y S V K T KQ I R R 18 7846 33 E I S F N A C L S H M F F I K 17 7847 62 F D R F V AV S N P L R Y A M 17 7848 127 M K L S C T D T R I N S A V G 17 7849 222Y L L I S P L M N P V I Y S V 17 7850 157 L L S Y V L I I R T V L S V A16 7851 197 L I S L S I V H R F G K Q A P 16 7852 212 A Y V H T M I A NT Y L L I S 16 7853 28 W F N V R E I S F N A C L S H 15 7854 29 F N V RE I S F N A C L S H M 15 7855 152 D L L L I L L S Y V L I I R T 15 7856169 S V A S P E E R K E T F S T C 15 7857 20 L V T M L S I F W F N V R EI 14 7858 24 L S I F W F N V R E I S F N A 14 7859 25 S I F W F N V R EI S F N A C 14 7860 45 F I K F F T V M E S S V L L A 14 7861 48 F F T VM E S S V L L A M A F 14 7862 95 L L M L T P M V A L L I R L S 14 7863148 T V G V D L L L I L L S Y V L 14 7864 150 G V D L L L I L L S Y V LI I 14 7865 153 L L L I L L S Y V L I I R T V 14 7866 158 L S Y V L I IR T V L S V A S 14 7867 161 V L I I R T V L S V A S P E E 14 7868 194 YI P L I S L S I V H R F G K 14 7869 220 N T Y L L I S P L M N P V I Y 147870 221 T Y L L I S P L M N P V I Y S 14 7871 1 M Y Y F L S M L S A T DL G L 13 7872 47 K F F T V M E S S V L L A M A 13 7873 49 F T V M E S SV L L A M A F D 13 7874 53 E S S V L L A M A F D R F V A 13 7875 88 V AS V I R G L L M L T P M V 13 7876 89 A S V I R G L L M L T P M V A 137877 92 I R G L L M L T P M V A L L I 13 7878 98 L T P M V A L L I R L SY C H 13 7879 101 M V A L L I R L S Y C H S Q V 13 7880 112 H S Q V L HH S Y C Y H P D V 13 7881 154 L L I L L S Y V L I I R T V L 13 7882 164I R T V L S V A S P E E R K E 13 7883 214 V H T M I A N T Y L L I S P L13 7884 6 S M L S A T D L G L S I S T L 12 7885 10 A T D L G L S I S T LV T M L 12 7886 17 I S T L V T M L S I F W F N V 12 7887 69 S N P L R YA M I L T D S R I 12 7888 73 R Y A M I L T D S R I A Q I G 12 7889 75 AM I L T D S R I A Q I G V A 12 7890 80 D S R I A Q I G V A S V I R G 127891 102 V A L L I R L S Y C H S Q V L 12 7892 103 A L L I R L S Y C H SQ V L H 12 7893 119 S Y C Y H P D V M K L S C T D 12 7894 124 P D V M KL S C T D T R I N S 12 7895 133 D T R I N S A V G L T A M F S 12 7896149 V G V D L L L I L L S Y V L I 12 7897 159 S Y V L I I R T V L S V AS P 12 7898 192 I Y Y I P L I S L S I V H R F 12 7899 230 N P V I Y S VK T K Q I R R A 12 7900 5 L S M L S A T D L G L S I S T 11 7901 9 S A TD L G L S I S T L V T M 11 7902 12 D L G L S I S T L V T M L S I 11 790313 L G L S I S T L V T M L S I F 11 7904 14 G L S I S T L V T M L S I FW 11 7905 21 V T M L S I F W F N V R E I S 11 7906 31 V R E I S F N A CL S H M F F 11 7907 40 L S H M F F I K F F T V M E S 11 7908 43 M F F IK F F T V M E S S V L 11 7909 55 S V L L A M A F D R F V A V S 11 791083 I A Q I G V A S V I R G L L M 11 7911 87 G V A S V I R G L L M L T PM 11 7912 123 H P D V M K L S C T D T R I N 11 7913 131 C T D T R I N SA V G L T A M 11 7914 137 N S A V G L T A M F S T V G V 11 7915 139 A VG L T A M F S T V G V D L 11 7916 144 A M F S T V G V D L L L I L L 117917 147 S T V G V D L L L I L L S Y V 11 7918 155 L I L L S Y V L I I RT V L S 11 7919 160 Y V L I I R T V L S V A S P E 11 7920 165 R T V L SV A S P E E R K E T 11 7921 181 S T C V S H I V A F A I Y Y I 11 7922184 V S H I V A F A I Y Y I P L I 11 7923 199 S L S I V H R F G K Q A PA Y 11 7924 215 H T M I A N T Y L L I S P L M 11 7925 226 S P L M N P VI Y S V K T K Q 11 7926 233 I Y S V K T K Q I R R A V I K 11 7927 16 S IS T L V T M L S I F W F N 10 7928 23 M L S I F W F N V R E I S F N 107929 42 H M F F I K F F T V M E S S V 10 7930 51 V M E S S V L L A M A FD R F 10 7931 111 C H S Q V L H H S Y C Y H P D 10 7932 113 S Q V L H HS Y C Y H P D V M 10 7933 126 V M K L S C T D T R I N S A V 10 7934 135R I N S A V G L T A M F S T V 10 7935 179 T F S T C V S H I V A F A I Y10 7936 185 S H I V A F A I Y Y I P L I S 10 7937 217 M I A N T Y L L IS P L M N P 10 7938 223 L L I S P L M N P V I Y S V K 10 7939 225 I S PL M N P V I Y S V K T K 10 7940 26 I F W F N V R E I S F N A C L 9 794134 I S F N A C L S H M F F I K F 9 7942 38 A C L S H M F F I K F F T V M9 7943 59 A M A F D R F V A V S N P L R 9 7944 61 A F D R F V A V S N PL R Y A 9 7945 67 A V S N P L R Y A M I L T D S 9 7946 84 A Q I G V A SV I R G L L M L 9 7947 97 M L T P M V A L L I R L S Y C 9 7948 106 I R LS Y C H S Q V L H H S Y 9 7949 109 S Y C H S Q V L H H S Y C Y H 9 7950118 H S Y C Y H P D V M K L S C T 9 7951 182 T C V S H I V A F A I Y Y IP 9 7952 183 C V S H I V A F A I Y Y I P L 9 7953 187 I V A F A I Y Y IP L I S L S 9 7954 201 S I V H R F G K Q A P A Y V H 9 7955 202 I V H RF G K Q A P A Y V H T 9 7956 203 V H R F G K Q A P A Y V H T M 9 7957213 Y V H T M I A N T Y L L I S P 9 7958 22 T M L S I F W F N V R E I SF 8 7959 41 S H M F F I K F F T V M E S S 8 7960 166 T V L S V A S P E ER K E T F 8 7961 168 L S V A S P E E R K E T F S T 8 7962 170 V A S P EE R K E T F S T C V 8 7963 177 K E T F S T C V S H I V A F A 8 7964 186H I V A F A I Y Y I P L I S L 8 7965 232 V I Y S V K T K Q I R R A V I 87966 234 Y S V K T K Q I R R A V I K I 8 7967 235 S V K T K Q I R R A VI K I L 8 7968 239 K Q I R R A V I K I L H S K E 8 7969 120 Y C Y H P DV M K L S C T D T 7 7970 129 L S C T D T R I N S A V G L T 7 7971 231 PV I Y S V K T K Q I R R A V 7 7972 39 C L S H M F F I K F F T V M E 67973 56 V L L A M A F D R F V A V S N 6 7974 77 I L T D S R I A Q I G VA S V 6 7975 11 T D L G L S I S T L V T M L S 5 7976 219 A N T Y L L I SP L M N P V I 5 7977 91 V I R G L L M L T P M V A L L 4 7978 224 L I S PL M N P V I Y S V K T 4 7979 15 L S I S T L V T M L S I F W F 3 7980 30N V R E I S F N A C L S H M F 3 7981 36 F N A C L S H M F F I K F F T 37982 50 T V M E S S V L L A M A F D R 3 7983 52 M E S S V L L A M A F DR F V 3 7984 64 R F V A V S N P L R Y A M I L 3 7985 68 V S N P L R Y AM I L T D S R 3 7986 79 T D S R I A Q I G V A S V I R 3 7987 100 P M V AL L I R L S Y C H S Q 3 7988 104 L L I R L S Y C H S Q V L H H 3 7989122 Y H P D V M K L S C T D T R I 3 7990 125 D V M K L S C T D T R I N SA 3 7991 140 V G L T A M F S T V G V D L L 3 7992 145 M F S T V G V D LL L I L L S 3 7993 162 L I I R T V L S V A S P E E R 3 7994 180 F S T CV S H I V A F A I Y Y 3 7995 191 A I Y Y I P L I S L S I V H R 3 7996193 Y Y I P L I S L S I V H R F G 3 7997 196 P L I S L S I V H R F G K QA 3 7998 210 A P A Y V H T M I A N T Y L L 3 7999 3 Y F L S M L S A T DL G L S I 2 8000 7 M L S A T D L G L S I S T L V 2 8001 8 L S A T D L GL S I S T L V T 2 8002 27 F W F N V R E I S F N A C L S 2 8003 60 M A FD R F V A V S N P L R Y 2 8004 66 V A V S N P L R Y A M I L T D 2 800571 P L R Y A M I L T D S R I A Q 2 8006 76 M I L T D S R I A Q I G V A S2 8007 82 R I A Q I G V A S V I R G L L 2 8008 86 I G V A S V I R G L LM L T P 2 8009 96 L M L T P M V A L L I R L S Y 2 8010 117 H H S Y C Y HP D V M K L S C 2 8011 128 K L S C T D T R I N S A V G L 2 8012 130 S CT D T R I N S A V G L T A 2 8013 132 T D T R I N S A V G L T A M F 28014 134 T R I N S A V G L T A M F S T 2 8015 138 S A V G L T A M F S TV G V D 2 8016 163 I I R T V L S V A S P E E R K 2 8017 173 P E E R K ET F S T C V S H I 2 8018 175 E R K E T F S T C V S H I V A 2 8019 178 ET F S T C V S H I V A F A I 2 8020 188 V A F A I Y Y I P L I S L S I 28021 190 F A I Y Y I P L I S L S I V H 2 8022 198 I S L S I V H R F G KQ A P A 2 8023 204 H R F G K Q A P A Y V H T M I 2 8024 218 I A N T Y LL I S P L M N P V 2 8025 227 P L M N P V I Y S V K T K Q I 2 8026 228 LM N P V I Y S V K T K Q I R 2 8027 237 K T K Q I R R A V I K I L H S 28028 240 Q I R R A V I K I L H S K E T 2 8029 19 T L V T M L S I F W F NV R E 1 8030 35 S F N A C L S H M F F I K F F 1 8031 58 L A M A F D R FV A V S N P L 1 8032 78 L T D S R I A Q I G V A S V I 1 8033 90 S V I RG L L M L T P M V A L 1 8034 107 R L S Y C H S Q V L H H S Y C 1 8035108 L S Y C H S Q V L H H S Y C Y 1 8036 114 Q V L H H S Y C Y H P D V MK 1 8037 121 C Y H P D V M K L S C T D T R 1 8038 136 I N S A V G L T AM F S T V G 1 8039 171 A S P E E R K E T F S T C V S 1 8040 172 S P E ER K E T F S T C V S H 1 8041 174 E E R K E T F S T C V S H I V 1 8042176 R K E T F S T C V S H I V A F 1 8043 205 R F G K Q A P A Y V H T M IA 1 8044 206 F G K Q A P A Y V H T M I A N 1 8045 209 Q A P A Y V H T MI A N T Y L 1 8046 216 T M I A N T Y L L I S P L M N 1 8047 236 V K T KQ I R R A V I K I L H 1 8048 HLA-DRB1*0401 (DR4Dw4) 15 - mers v.1:238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score SEQ ID 157 L L S Y V L II R T V L S V A 28 8049 191 A I Y Y I P L I S L S I V H R 28 8050 14 G LS I S T L V T M L S I F W 26 8051 74 Y A M I L T D S R I A Q I G V 268052 85 Q I G V A S V I R G L L M L T 26 8053 151 V D L L L I L L S Y VL I I R 26 8054 158 L S Y V L I I R T V L S V A S 26 8055 161 V L I I RT V L S V A S P E E 26 8056 197 L I S L S I V H R F G K Q A P 26 8057222 Y L L I S P L M N P V I Y S V 26 8058 230 N P V I Y S V K T K Q I RR A 26 8059 24 L S I F W F N V R E I S F N A 22 8060 42 H M F F I K F FT V M E S S V 22 8061 45 F I K F F T V M E S S V L L A 22 8062 46 I K FF T V M E S S V L L A M 22 8063 59 A M A F D R F V A V S N P L R 22 806462 F D R F V A V S N P L R Y A M 22 8065 71 P L R Y A M I L T D S R I AQ 22 8066 119 S Y C Y H P D V M K L S C T D 22 8067 143 T A M F S T V GV D L L L I L 22 8068 177 K E T F S T C V S H I V A F A 22 8069 219 A NT Y L L I S P L M N P V I 22 8070 2 Y Y F L S M L S A T D L G L S 208071 4 F L S M L S A T D L G L S I S 20 8072 10 A T D L G L S I S T L VT M L 20 8073 20 L V T M L S I F W F N V R E I 20 8074 23 M L S I F W FN V R E I S F N 20 8075 40 L S H M F F I K F F T V M E S 20 8076 43 M FF I K F F T V M E S S V L 20 8077 55 S V L L A M A F D R F V A V S 208078 57 L L A M A F D R F V A V S N P 20 8079 65 F V A V S N P L R Y A MI L T 20 8080 73 R Y A M I L T D S R I A Q I G 20 8081 80 D S R I A Q IG V A S V I R G 20 8082 92 I R G L L M L T P M V A L L I 20 8083 98 L TP M V A L L I R L S Y C H 20 8084 99 T P M V A L L I R L S Y C H S 208085 102 V A L L I R L S Y C H S Q V L 20 8086 105 L I R L S Y C H S Q VL H H S 20 8087 123 H P D V M K L S C T D T R I N 20 8088 126 V M K L SC T D T R I N S A V 20 8089 133 D T R I N S A V G L T A M F S 20 8090146 F S T V G V D L L L I L L S Y 20 8091 148 T V G V D L L L I L L S YV L 20 8092 150 G V D L L L I L L S Y V L I I 20 8093 152 D L L L I L LS Y V L I I R T 20 8094 155 L I L L S Y V L I I R T V L S 20 8095 164 IR T V L S V A S P E E R K E 20 8096 181 S T C V S H I V A F A I Y Y I 208097 184 V S H I V A F A I Y Y I P L I 20 8098 189 A F A I Y Y I P L I SL S I V 20 8099 192 I Y Y I P L I S L S I V H R F 20 8100 226 S P L M NP V I Y S V K T K Q 20 8101 238 T K Q I R R A V I K I L H S K 20 8102 11T D L G L S I S T L V T M L S 18 8103 27 F W F N V R E I S F N A C L S18 8104 47 K F F T V M E S S V L L A M A 18 8105 56 V L L A M A F D R FV A V S N 18 8106 61 A F D R F V A V S N P L R Y A 18 8107 77 I L T D SR I A Q I G V A S V 18 8108 127 M K L S C T D T R I N S A V G 18 8109140 V G L T A M F S T V G V D L L 18 8110 168 L S V A S P E E R K E T FS T 18 8111 174 E E R K E T F S T C V S H I V 18 8112 178 E T F S T C VS H I V A F A I 18 8113 208 K Q A P A Y V H T M I A N T Y 18 8114 212 AY V H T M I A N T Y L L I S 18 8115 213 Y V H T M I A N T Y L L I S P 188116 218 I A N T Y L L I S P L M N P V 18 8117 227 P L M N P V I Y S V KT K Q I 18 8118 235 S V K T K Q I R R A V I K I L 18 8119 1 M Y Y F L SM L S A T D L G L 16 8120 25 S I F W F N V R E I S F N A C 16 8121 33 EI S F N A C L S H M F F I K 16 8122 117 H H S Y C Y H P D V M K L S C 168123 187 I V A F A I Y Y I P L I S L S 16 8124 190 F A I Y Y I P L I S LS I V H 16 8125 203 V H R F G K Q A P A Y V H T M 16 8126 210 A P A Y VH T M I A N T Y L L 16 8127 5 L S M L S A T D L G L S I S T 14 8128 12 DL G L S I S T L V T M L S I 14 8129 17 I S T L V T M L S I F W F N V 148130 18 S T L V T M L S I F W F N V R 14 8131 21 V T M L S I F W F N V RE I S 14 8132 28 W F N V R E I S F N A C L S H 14 8133 48 F F T V M E SS V L L A M A F 14 8134 49 F T V M E S S V L L A M A F D 14 8135 53 E SS V L L A M A F D R F V A 14 8136 69 S N P L R Y A M I L T D S R I 148137 75 A M I L T D S R I A Q I G V A 14 8138 83 I A Q I G V A S V I R GL L M 14 8139 88 V A S V I R G L L M L T P M V 14 8140 89 A S V I R G LL M L T P M V A 14 8141 93 R G L L M L T P M V A L L I R 14 8142 94 G LL M L T P M V A L L I R L 14 8143 95 L L M L T P M V A L L I R L S 148144 103 A L L I R L S Y C H S Q V L H 14 8145 124 P D V M K L S C T D TR I N S 14 8146 137 N S A V G L T A M F S T V G V 14 8147 139 A V G L TA M F S T V G V D L 14 8148 142 L T A M F S T V G V D L L L I 14 8149153 L L L I L L S Y V L I I R T V 14 8150 160 Y V L I I R T V L S V A SP E 14 8151 165 R T V L S V A S P E E R K E T 14 8152 185 S H I V A F AI Y Y I P L I S 14 8153 194 Y I P L I S L S I V H R F G K 14 8154 200 LS I V H R F G K Q A P A Y V 14 8155 214 V H T M I A N T Y L L I S P L 148156 215 H T M I A N T Y L L I S P L M 14 8157 221 T Y L L I S P L M N PV I Y S 14 8158 225 I S P L M N P V I Y S V K T K 14 8159 229 M N P V IY S V K T K Q I R R 14 8160 6 S M L S A T D L G L S I S I L 12 8161 7 ML S A T D L G L S I S T L V 12 8162 8 L S A T D L G L S I S T L V T 128163 9 S A T D L G L S I S T L V T M 12 8164 15 L S I S T L V T M L S IF W F 12 8165 29 F N V R E I S F N A C L S H M 12 8166 30 N V R E I S FN A C L S H M F 12 8167 32 R E I S F N A C L S H M F F I 12 8168 34 I SF N A C L S H M F F I K F 12 8169 39 C L S H M F F I K F F T V M E 128170 50 T V M E S S V L L A M A F D R 12 8171 66 V A V S N P L R Y A M IL T D 12 8172 72 L R Y A M I L T D S R I A Q I 12 8173 78 L T D S R I AQ I G V A S V I 12 8174 82 R I A Q I G V A S V I R G L L 12 8175 86 I GV A S V I R G L L M L T P 12 8176 90 S V I R G L L M L T P M V A L 128177 91 V I R G L L M L T P M V A L L 12 8178 97 M L T P M V A L L I R LS Y C 12 8179 104 L L I R L S Y C H S Q V L H H 12 8180 109 S Y C H S QV L H H S Y C Y H 12 8181 110 Y C H S Q V L H H S Y C Y H P 12 8182 115V L H H S Y C Y H P D V M K L 12 8183 130 S C T D T R I N S A V G L T A12 8184 134 T R I N S A V G L T A M F S T 12 8185 136 I N S A V G L T AM F S T V G 12 8186 138 S A V G L T A M F S T V G V D 12 8187 145 M F ST V G V D L L L I L L S 12 8188 147 S T V G V D L L L I L L S Y V 128189 156 I L L S Y V L I I R T V L S V 12 8190 173 P E E R K E T F S T CV S H I 12 8191 186 H I V A F A I Y Y I P L I S L 12 8192 196 P L I S LS I V H R F G K Q A 12 8193 201 S I V H R F G K Q A P A Y V H 12 8194206 F G K Q A P A Y V H T M I A N 12 8195 207 G K Q A P A Y V H T M I AN T 12 8196 217 M I A N T Y L L I S P L M N P 12 8197 234 Y S V K T K QI R R A V I K I 12 8198 240 Q I R R A V I K I L H S K E T 12 8199 26 I FW F N V R E I S F N A C L 11 8200 41 S H M F F I K F F T V M E S S 118201 107 R L S Y C H S Q V L H H S Y C 10 8202 101 M V A L L I R L S Y CH S Q V 9 8203 159 S Y V L I I R T V L S V A S P 9 8204 199 S L S I V HR F G K Q A P A Y 9 8205 233 I Y S V K T K Q I R R A V I K 9 8206 31 V RE I S F N A C L S H M F F 8 8207 37 N A C L S H M F F I K F F T V 8 820854 S S V L L A M A F D R F V A V 8 8209 63 D R F V A V S N P L R Y A M I8 8210 112 H S Q V L H H S Y C Y H P D V 8 8211 113 S Q V L H H S Y C YH P D V M 8 8212 154 L L I L L S Y V L I I R T V L 8 8213 167 V L S V AS P F E R K E T F S 8 8214 195 I P L I S L S I V H R F G K Q 8 8215 211P A Y V H T M I A N T Y L L I 8 8216 220 N T Y L L I S P L M N P V I Y 88217 129 L S C T D T R I N S A V G L T 7 8218 171 A S P E E R K E T F ST C V S 7 8219 3 Y F L S M L S A T D L G L S I 6 8220 13 L G L S I S T LV T M L S I F 6 8221 19 T L V T M L S I F W F N V R E 6 8222 22 T M L SI F W F N V R E I S F 6 8223 35 S F N A C L S H M F F I K F F 6 8224 36F N A C L S H M F F I K F F T 6 8225 38 A C L S H M F F I K F F T V M 68226 44 F F I K F F T V M E S S V L L 6 8227 51 V M E S S V L L A M A FD R F 6 8228 52 M E S S V L L A M A F D R F V 6 8229 60 M A F D R F V AV S N P L R Y 6 8230 64 R F V A V S N P L R Y A M I L 6 8231 68 V S N PL R Y A M I L T D S R 6 8232 70 N P L R Y A M I L T D S R I A 6 8233 79T D S R I A Q I G V A S V I R 6 8234 81 S R I A Q I G V A S V I R G L 68235 84 A Q I G V A S V I R G L L M L 6 8236 96 L M L T P M V A L L I RL S Y 6 8237 100 P M V A L L I R L S Y C H S Q 6 8238 106 I R L S Y C HS Q V L H H S Y 6 8239 108 L S Y C H S Q V L H H S Y C Y 6 8240 111 C HS Q V L H H S Y C Y H P D 6 8241 116 L H H S Y C Y H P D V M K L S 68242 118 H S Y C Y H P D V M K L S C T 6 8243 120 Y C Y H P D V M K L SC T D T 6 8244 121 C Y H P D V M K L S C T D T R 6 8245 125 D V M K L SC T D T R I N S A 6 8246 128 K L S C T D T R I N S A V G L 6 8247 131 CT D T R I N S A V G L T A M 6 8248 132 T D T R I N S A V G L T A M F 68249 135 R I N S A V G L T A M F S T V 6 8250 144 A M F S T V G V D L LL I L L 6 8251 149 V G V D L L L I L L S Y V L I 6 8252 162 L I I R T VL S V A S P E E R 6 8253 166 T V L S V A S P E E R K E T F 6 8254 169 SV A S P E E R K E T F S T C 6 8255 172 S P E E R K E T F S T C V S H 68256 176 R K E T F S T C V S H I V A F 6 8257 180 F S T C V S H I V A FA I Y Y 6 8258 182 T C V S H I V A F A I Y Y I P 6 8259 183 C V S H I VA F A I Y Y I P L 6 8260 188 V A F A I Y Y I P L I S L S I 6 8261 193 YY I P L I S L S I V H R F G 6 8262 198 I S L S I V H R F G K Q A P A 68263 204 H R F G K Q A P A Y V H T M I 6 8264 205 R F G K Q A P A Y V HT M I A 6 8265 209 Q A P A Y V H T M I A N T Y L 6 8266 224 L I S P L MN P V I Y S V K T 6 8267 228 L M N P V I Y S V K T K Q I R 6 8268 232 VI Y S V K T K Q I R R A V I 6 8269 239 K Q I R R A V I K I L H S K E 68270 231 P V I Y S V K T K Q I R R A V 5 8271 58 L A M A F D R F V A V SN P L 1 8272 67 A V S N P L R Y A M I L T D S 1 8273 87 G V A S V I R GL L M L T P M 1 8274 122 Y H P D V M K L S C T D T R I 1 8275 170 V A SP E E R K E T F S T C V 1 8276 236 V K T K Q I R R A V I K I L H 1 8277237 K T K Q I R R A V I K I L H S 1 8278 76 M I L T D S R I A Q I G V AS −5 8279 202 I V H R F G K Q A P A Y V H T −5 8280 HLA-DRB1*1101 15 -mers v.1: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score SEQ ID 24 L SI F W F N V R E I S F N A 27 8281 157 L L S Y V L I I R T V L S V A 258282 178 E T F S T C V S H I V A F A I 23 8283 196 P L I S L S I V H R FG K Q A 23 8284 14 G L S I S T L V T M L S I F W 21 8285 85 Q I G V A SV I R G L L M L T 21 8286 139 A V G L T A M F S T V G V D L 21 8287 46 IK F F T V M E S S V L L A M 20 8288 98 L T P M V A L L I R L S Y C H 208289 99 T P M V A L L I R L S Y C H S 20 8290 197 L I S L S I V H R F GK Q A P 20 8291 200 L S I V H R F G K Q A P A Y V 20 8292 231 P V I Y SV K T K Q I R R A V 20 8293 92 I R G L L M L T P M V A L L I 19 8294 119S Y C Y H P D V M K L S C T D 19 8295 148 T V G V D L L L I L L S Y V L19 8296 158 L S Y V L I I R T V L S V A S 19 8297 89 A S V I R G L L M LT P M V A 18 8298 102 V A L L I R L S Y C H S Q V L 18 8299 161 V L I IR T V L S V A S P E E 18 8300 25 S I F W F N V R E I S F N A C 17 830145 F I K F F T V M E S S V L L A 17 8302 62 F D R F V A V S N P L R Y AM 17 8303 95 L L M L T P M V A L L I R L S 17 8304 143 T A M F S T V G VD L L L I L 17 8305 190 F A I Y Y I P L I S L S I V H 17 8306 229 M N PV I Y S V K T K Q I R R 17 8307 1 M Y Y F L S M L S A T D L G L 16 830871 P L R Y A M I L T D S R I A Q 16 8309 191 A I Y Y I P L I S L S I V HR 16 8310 219 A N T Y L L I S P L M N P V I 16 8311 7 M L S A T D L G LS I S T L V 15 8312 56 V L L A M A F D R F V A V S N 15 8313 83 I A Q IG V A S V I R G L L M 15 8314 110 Y C H S Q V L H H S Y C Y H P 15 8315130 S C T D T R I N S A V G L T A 15 8316 160 Y V L I I R T V L S V A SP E 15 8317 162 L I I R T V L S V A S P E E R 15 8318 233 I Y S V K T KQ I R R A V I K 15 8319 235 S V K T K Q I R R A V I K I L 15 8320 239 KQ I R R A V I K I L H S K E 15 8321 18 S T L V T M L S I F W F N V R 148322 34 I S F N A C L S H M F F I K F 14 8323 54 S S V L L A M A F D R FV A V 14 8324 65 F V A V S N P L R Y A M I L T 14 8325 73 R Y A M I L TD S R I A Q I G 14 8326 74 Y A M I L T D S R I A Q I G V 14 8327 109 S YC H S Q V L H H S Y C Y H 14 8328 120 Y C Y H P D V M K L S C T D T 148329 127 M K L S C T D T R I N S A V G 14 8330 133 D T R I N S A V G L TA M F S 14 8331 155 L I L L S Y V L I I R T V L S 14 8332 181 S T C V SH I V A F A I Y Y I 14 8333 5 L S M L S A T D L G L S I S T 13 8334 37 NA C L S H M F F I K F F T V 13 8335 40 L S H M F F I K F F T V M E S 138336 48 F F T V M E S S V L L A M A F 13 8337 151 V D L L L I L L S Y VL I I R 13 8338 152 D L L L I L L S Y V L I I R T 13 8339 177 K E T F ST C V S H I V A F A 13 8340 185 S H I V A F A I Y Y I P L I S 13 8341192 I Y Y I P L I S L S I V H R F 13 8342 208 K Q A P A Y V H T M I A NT Y 13 8343 215 H T M I A N T Y L L I S P L M 13 8344 222 Y L L I S P LM N P V I Y S V 13 8345 226 S P L M N P V I Y S V K T K Q 13 8346 240 QI R R A V I K I L H S K E T 13 8347 2 Y Y F L S M L S A T D L G L S 128348 17 I S T L V T M L S I F W F N V 12 8349 20 L V T M L S I F W F N VR E I 12 8350 28 W F N V R E I S F N A C L S H 12 8351 41 S H M F F I KF F T V M E S S 12 8352 43 M F F I K F F T V M E S S V L 12 8353 50 T VM E S S V L L A M A F D R 12 8354 59 A M A F D R F V A V S N P L R 128355 60 M A F D R F V A V S N P L R Y 12 8356 70 N P L R Y A M I L T D SR I A 12 8357 80 D S R I A Q I G V A S V I R G 12 8358 113 S Q V L H H SY C Y H P D V M 12 8359 123 H P D V M K L S C T D T R I N 12 8360 136 IN S A V G L T A M F S T V G 12 8361 150 G V D L L L I L L S Y V L I I 128362 164 I R T V L S V A S P E E R K E 12 8363 189 A F A I Y Y I P L I SL S I V 12 8364 194 Y I P L I S L S I V H R F G K 12 8365 199 S L S I VH R F G K Q A P A Y 12 8366 211 P A Y V H T M I A N T Y L L I 12 8367220 N T Y L L I S P L M N P V I Y 12 8368 230 N P V I Y S V K T K Q I RR A 12 8369 26 I F W F N V R E I S F N A C L 11 8370 187 I V A F A I Y YI P L I S L S 11 8371 234 Y S V K T K Q I R R A V I K I 11 8372 33 E I SF N A C L S H M F F I K 10 8373 42 H M F F I K F F T V M E S S V 10 8374107 R L S Y C H S Q V L H H S Y C 10 8375 117 H H S Y C Y H P D V M K LS C 10 8376 203 V H R F G K Q A P A Y V H T M 10 8377 207 G K Q A P A YV H T M I A N T 10 8378 210 A P A Y V H T M I A N T Y L L 10 8379 44 F FI K F F T V M E S S V L L 9 8380 63 D R F V A V S N P L R Y A M I 9 8381142 L T A M F S T V G V D L L L I 9 8382 154 L L I L L S Y V L I I R T VL 9 8383 238 T K Q I R R A V I K I L H S K 9 8384 15 L S I S T L V T M LS I F W F 8 8385 23 M L S I F W F N V R E I S F N 8 8386 39 C L S H M FF I K F F T V M E 8 8387 49 F T V M E S S V L L A M A F D 8 8388 58 L AM A F D R F V A V S N P L 8 8389 72 L R Y A M I L T D S R I A Q I 8 839075 A M I L T D S R I A Q I G V A 8 8391 86 I G V A S V I R G L L M L T P8 8392 104 L L I R L S Y C H S Q V L H H 8 8393 108 L S Y C H S Q V L HH S Y C Y 8 8394 115 V L H H S Y C Y H P D V M K L 8 8395 126 V M K L SC T D T R I N S A V 8 8396 128 K L S C T D T R I N S A V G L 8 8397 146F S T V G V D L L L I L L S Y 8 8398 156 I L L S Y V L I I R T V L S V 88399 167 V L S V A S P E E R K E T F S 8 8400 168 L S V A S P E E R K ET F S T 8 8401 169 S V A S P E E R K E T F S T C 8 8402 195 I P L I S LS I V H R F G K Q 8 8403 212 A Y V H T M I A N T Y L L I S 8 8404 217 MI A N T Y L L I S P L M N P 8 8405 225 I S P L M N P V I Y S V K T K 88406 227 P L M N P V I Y S V K T K Q I 8 8407 3 Y F L S M L S A T D L GL S I 7 8408 10 A T D L G L S I S T L V T M L 7 8409 11 T D L G L S I ST L V T M L S 7 8410 21 V T M L S I F W F N V R E I S 7 8411 30 N V R EI S F N A C L S H M F 7 8412 51 V M E S S V L L A M A F D R F 7 8413 55S V L L A M A F D R F V A V S 7 8414 64 R F V A V S N P L R Y A M I L 78415 76 M I L T D S R I A Q I G V A S 7 8416 78 L T D S R I A Q I G V AS V I 7 8417 82 R I A Q I G V A S V I R G L L 7 8418 88 V A S V I R G LL M L T P M V 7 8419 94 G L L M L T P M V A L L I R L 7 8420 96 L M L TP M V A L L I R L S Y 7 8421 105 L I R L S Y C H S Q V L H H S 7 8422121 C Y H P D V M K L S C T D T R 7 8423 145 M F S T V G V D L L L I L LS 7 8424 147 S T V G V D L L L I L L S Y V 7 8425 153 L L L I L L S Y VL I I R T V 7 8426 165 R T V L S V A S P E E R K E T 7 8427 174 E E R KE T F S T C V S H I V 7 8428 182 T C V S H I V A F A I Y Y I P 7 8429186 H I V A F A I Y Y I P L I S L 7 8430 188 V A F A I Y Y I P L I S L SI 7 8431 214 V H T M I A N T Y L L I S P L 7 8432 218 I A N T Y L L I SP L M N P V 7 8433 223 L L I S P L M N P V I Y S V K 7 8434 4 F L S M LS A T D L G L S I S 6 8435 9 S A T D L G L S I S T L V T M 6 8436 12 D LG L S I S T L V T M L S I 6 8437 27 F W F N V R E I S F N A C L S 6 843831 V R E I S F N A C L S H M F F 6 8439 52 M E S S V L L A M A F D R F V6 8440 53 E S S V L L A M A F D R F V A 6 8441 57 L L A M A F D R F V AV S N P 6 8442 66 V A V S N P L R Y A M I L T D 6 8443 69 S N P L R Y AM I L T D S R I 6 8444 77 I L T D S R I A Q I G V A S V 6 8445 79 T D SR I A Q I G V A S V I R 6 8446 90 S V I R G L L M L T P M V A L 6 844791 V I R G L L M L T P M V A L L 6 8448 93 R G L L M L T P M V A L L I R6 8449 100 P M V A L L I R L S Y C H S Q 6 8450 101 M V A L L I R L S YC H S Q V 6 8451 103 A L L I R L S Y C H S Q V L H 6 8452 112 H S Q V LH H S Y C Y H P D V 6 8453 124 P D V M K L S C T D T R I N S 6 8454 134T R I N S A V G L T A M F S T 6 8455 137 N S A V G L T A M F S T V G V 68456 144 A M F S T V G V D L L L I L L 6 8457 149 V G V D L L L I L L SY V L I 6 8458 159 S Y V L I I R T V L S V A S P 6 8459 170 V A S P E ER K E T F S T C V 6 8460 180 F S T C V S H I V A F A I Y Y 6 8461 184 VS H I V A F A I Y Y I P L I 6 8462 201 S I V H R F G K Q A P A Y V H 68463 216 T M I A N T Y L L I S P L M N 6 8464 221 T Y L L I S P L M N PV I Y S 6 8465 224 L I S P L M N P V I Y S V K T 6 8466 61 A F D R F V AV S N P L R Y A 4 8467 81 S R I A Q I G V A S V I R G L 3 8468 84 A Q IG V A S V I R G L L M L 3 8469 97 M L T P M V A L L I R L S Y C 3 847016 S I S T L V T M L S I F W F N 2 8471 22 T M L S I F W F N V R E I S F2 8472 125 D V M K L S C T D T R I N S A 2 8473 163 I I R T V L S V A SP E E R K 2 8474 166 T V L S V A S P E E R K E T F 2 8475 175 E R K E TF S T C V S H I V A 2 8476 198 I S L S I V H R F G K Q A P A 2 8477 232V I Y S V K T K Q I R R A V I 2 8478 32 R E I S F N A C L S H M F F I 18479 36 F N A C L S H M F F I K F F T 1 8480 47 K F F T V M E S S V L LA M A 1 8481 67 A V S N P L R Y A M I L T D S 1 8482 68 V S N P L R Y AM I L T D S R 1 8483 106 I R L S Y C H S Q V L H H S Y 1 8484 116 L H HS Y C Y H P D V M K L S 1 8485 118 H S Y C Y H P D V M K L S C T 1 8486132 T D T R I N S A V G L T A M F 1 8487 135 R I N S A V G L T A M F S TV 1 8488 141 G L T A M F S T V G V D L L L 1 8489 176 R K E T F S T C VS H I V A F 1 8490 179 T F S T C V S H I V A F A I Y 1 8491 183 C V S HI V A F A I Y Y I P L 1 8492 193 Y Y I P L I S L S I V H R F G 1 8493202 I V H R F G P Q A P A Y V H T 8494 part 2 H2-Ak 15 - mers, v.1B Pos1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score SEQ ID 2 I T S T L Q N I T S T S I IF 16 8495 15 I F L L T G V P G L E A F H T 16 8496 48 L I L F A T I T QP S L H E P 14 8497 53 T I T Q P S L H E P M Y Y F L 14 8498 61 E P M YY F L S M L S A T D L 14 8499 43 L L G N S L I L F A T I T Q P 12 850012 T S I I F L L T G V P G L E A 10 8501 21 V P G L E A F H T W I S I PF 10 8502 47 S L I L F A T I T Q P S L H E 10 8503 8 N I T S T S I I F LL T G V P 8 8504 9 I T S T S I I F L L T G V P G 8 8505 11 S T S I I F LL T G V P G L E 8 8506 17 L L T G V P G L E A F H T W I 8 8507 18 L T GV P G L E A F H T W I S 8 8508 28 H T W I S I P F C F L S V T A 8 850931 I S I P F C F L S V T A L L G 8 8510 34 P F C F L S V T A L L G N S L8 8511 36 C F L S V T A L L G N S L I L 8 8512 37 F L S V T A L L G N SL I L F 8 8513 41 T A L L G N S L I L F A T I T 8 8514 42 A L L G N S LI L F A T I T Q 8 8515 44 L G N S L I L F A T I T Q P S 8 8516 57 P S LH E P M Y Y F L S M L S 8 8517 60 H E P M Y Y F L S M L S A T D 8 8518 3T S T L Q N I T S T S I I F L 6 8519 5 T L Q N I T S T S I I F L L T 68520 25 E A F H T W I S I P F C F L S 6 8521 27 F H T W I S I P F C F LS V T 6 8522 32 S I P F C F L S V T A L L G N 6 8523 38 L S V T A L L GN S L I L F A 6 8524 40 V T A L L G N S L I L F A T I 6 8525 45 G N S LI L F A T I T Q P S L 4 8526 1 F I T S T L Q N I T S T S I I 2 8527 4 ST L Q N I T S T S I I F L L 2 8528 30 W I S I P F C F L S V T A L L 28529 33 I P F C F L S V T A L L G N S 2 8530 62 P M Y Y F L S M L S A TD L G 2 8531 H2-Ek 15 - mers, v.1B Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5score SEQ ID 12 T S I I F L L T G V P G L E A 20 8532 15 I F L L T G V PG L E A F H T 20 8533 18 L T G V P G L E A F H T W I S 20 8534 37 F L SV T A L L G N S L I L F 20 8535 3 T S T L Q N I T S T S I I F L 16 853611 S T S I I F L L T G V P G L E 16 8537 21 V P G L E A F H T W I S I PF 16 8538 34 P F C F L S V T A L L G N S L 16 8539 41 T A L L G N S L IL F A T I T 16 8540 45 G N S L I L F A T I T Q P S L 16 8541 48 L I L FA T I T Q P S L H E P 16 8542 27 F H T W I S I P F C F L S V T 12 854332 S I P F C F L S V T A L L G N 12 8544 61 E P M Y Y F L S M L S A T DL 12 8545 62 P M Y Y F L S M L S A T D L G 12 8546 6 L Q N I T S T S I IF L L T G 10 8547 14 I I F L L T G V P G L E A F H 10 8548 28 H T W I SI P F C F L S V T A 10 8549 30 W I S I P F C F L S V T A L L 10 8550 35F C F L S V T A L L G N S L I 10 8551 38 L S V T A L L G N S L I L F A10 8552 40 V T A L L G N S L I L F A T I 10 8553 44 L G N S L I L F A TI T Q P S 10 8554 46 N S L I L F A T I T Q P S L H 10 8555 47 S L I L FA T I T Q P S L H E 10 8556 51 F A T I T Q P S L H E P M Y Y 10 8557 53T I T Q P S L H E P M Y Y F L 10 8558 56 Q P S L H E P M Y Y F L S M L10 8559 5 T L Q N I T S T S I I F L L T 6 8560 7 Q N I T S T S I I F L LT G V 6 8561 8 N I T S T S I I F L L T G V P 6 8562 9 I T S T S I I F LL T G V P G 6 8563 10 T S T S I I F L L T G V P G L 6 8564 13 S I I F LL T G V P G L E A F 6 8565 24 L E A F H T W I S I P F C F L 6 8566 25 EA F H T W I S I P F C F L S 6 8567 26 A F H T W I S I P F C F L S V 68568 29 T W I S I P F C F L S V T A L 6 8569 31 I S I P F C F L S V T AL L G 6 8570 33 I P F C F L S V T A L L G N S 6 8571 42 A L L G N S L IL F A T I T Q 6 8572 43 L L G N S L I L F A T I T Q P 6 8573 52 A T I TQ P S L H E P M Y Y F 6 8574 60 H E P M Y Y F L S M L S A T D 6 8575 17L L T G V P G L E A F H T W I 4 8576 HLA-DRB1*0101 15 - mers, v.1B:238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score SEQ ID 37 F L S V T A LL G N S L I L F 33 8577 11 S T S I I F L L T G V P G L E 31 8578 15 I FL L T G V P G L E A F H T 31 8579 3 T S T L Q N I T S T S I I F L 298580 32 S I P F C F L S V T A L L G N 28 8581 61 E P M Y Y F L S M L S AT D L 27 8582 12 T S I I F L L T G V P G L E A 25 8583 18 L T G V P G LE A F H T W I S 25 8584 24 L E A F H T W I S I P F C F L 24 8585 27 F HT W I S I P F C F L S V T 24 8586 34 P F C F L S V T A L L G N S L 248587 48 L I L F A T I T Q P S L H E P 24 8588 13 S I I F L L T G V P G LE A F 22 8589 21 V P G L E A F H T W I S I P F 22 8590 47 S L I L F A TI T Q P S L H E 22 8591 60 H E P M Y Y F L S M L S A T D 22 8592 44 L GN S L I L F A T I T Q P S 20 8593 28 H T W I S I P F C F L S V T A 198594 4 S T L Q N I T S T S I I F L L 18 8595 38 L S V T A L L G N S L IL F A 18 8596 46 N S L I L F A T I T Q P S L H 18 8597 6 L Q N I T S T SI I F L L T G 17 8598 26 A F H T W I S I P F C F L S V 17 8599 51 F A TI T Q P S L H E P M Y Y 17 8600 40 V T A L L G N S L I L F A T I 16 860141 T A L L G N S L I L F A T I T 16 8602 56 Q P S L H E P M Y Y F L S ML 16 8603 33 I P F C F L S V T A L L G N S 15 8604 39 S V T A L L G N SL I L F A T 15 8605 43 L L G N S L I L F A T I T Q P 15 8606 45 G N S LI L F A T I T Q P S L 15 8607 2 I T S T L Q N I T S T S I I F 14 8608 5T L Q N I T S T S I I F L L T 14 8609 10 T S T S I I F L L T G V P G L14 8610 14 I I F L L T G V P G L E A F H 14 8611 31 I S I P F C F L S VT A L L G 14 8612 57 P S L H E P M Y Y F L S M L S 14 8613 50 L F A T IT Q P S L H E P M Y 12 8614 62 P M Y Y F L S M L S A T D L G 11 8615 35F C F L S V T A L L G N S L I 10 8616 49 I L F A T I T Q P S L H E P M10 8617 1 F I T S T L Q N I T S T S I I 9 8618 9 I T S T S I I F L L T GV P G 9 8619 16 F L L T G V P G L E A F H T W 9 8620 20 G V P G L E A FH T W I S I P 9 8621 22 P G L E A F H T W I S I P F C 9 8622 30 W I S IP F C F L S V T A L L 9 8623 36 C F L S V T A L L G N S L I L 9 8624 42A L L G N S L I L F A T I T Q 9 8625 58 S L H E P M Y Y F L S M L S A 98626 7 Q N I T S T S I I F L L T G V 8 8627 23 G L E A F H T W I S I P FC F 8 8628 29 T W I S I P F C F L S V T A L 8 8629 52 A T I T Q P S L HE P M Y Y F 8 8630 53 T I T Q P S L H E P M Y Y F L 8 8631 54 I T Q P SL H E P M Y Y F L S 8 8632 55 T Q P S L H E P M Y Y F L S M 8 8633 59 LH E P M Y Y F L S M L S A T 8 8634 8 N I T S T S I I F L L T G V P 78635 25 E A F H T W I S I P F C F L S 7 8636 17 L L T G V P G L E A F HT W I 1 8637 19 T G V P G L E A F H T W I S I 1 8638 HLA-DRB1*0301(DR17) 15 - mers, v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 scoreSEQ ID 40 V T A L L G N S L I L F A T I 22 8639 48 L I L F A T I T Q P SL H E P 22 8640 6 L Q N I T S T S I I F L L T G 21 8641 37 F L S V T A LL G N S L I L F 21 8642 13 S I I F L L T G V P G L E A F 20 8643 56 Q PS L H E P M Y Y F L S M L 19 8644 32 S I P F C F L S V T A L L G N 188645 24 L E A F H T W I S I P F C F L 16 8646 53 T I T Q P S L H E P M YY F L 15 8647 14 I I F L L T G V P G L E A F H 13 8648 15 I F L L T G VP G L E A F H T 13 8649 34 P F C F L S V T A L L G N S L 13 8650 11 S TS I I F L L T G V P G L E 12 8651 12 T S I I F L L T G V P G L E A 128652 39 S V T A L L G N S L I L F A T 12 8653 41 T A L L G N S L I L F AT I T 12 8654 45 G N S L I L F A T I T Q P S L 12 8655 46 N S L I L F AT I T Q P S L H 12 8656 51 F A T I T Q P S L H E P M Y Y 12 8657 60 H EP M Y Y F L S M L S A T D 12 8658 18 L T G V P G L E A F H T W I S 118659 27 F H T W I S I P F C F L S V T 11 8660 28 H T W I S I P F C F L SV T A 11 8661 33 I P F C F L S V T A L L G N S 11 8662 35 F C F L S V TA L L G N S L I 11 8663 47 S L I L F A T I T Q P S L H E 11 8664 55 T QP S L H E P M Y Y F L S M 11 8665 3 T S T L Q N I T S T S I I F L 108666 16 F L L T G V P G L E A F H T W 10 8667 17 L L T G V P G L E A F HT W I 10 8668 21 V P G L E A F H T W I S I P F 10 8669 30 W I S I P F CF L S V T A L L 10 8670 54 I T Q P S L H E P M Y Y F L S 10 8671 5 T L QN I T S T S I I F L L T 9 8672 7 Q N I T S T S I I F L L T G V 9 8673 38L S V T A L L G N S L I L F A 9 8674 26 A F H T W I S I P F C F L S V 88675 59 L H E P M Y Y F L S M L S A T 8 8676 8 N I T S T S I I F L L T GV P 4 8677 20 G V P G L E A F H T W I S I P 3 8678 29 T W I S I P F C FL S V T A L 3 8679 36 C F L S V T A L L G N S L I L 3 8680 43 L L G N SL I L F A T I T Q P 3 8681 50 L F A T I T Q P S L H E P M Y 3 8682 1 F IT S T L Q N I T S T S I I 2 8683 2 I T S T L Q N I T S T S I I F 2 868410 T S T S I I F L L T G V P G L 2 8685 25 E A F H T W I S I P F C F L S2 8686 31 I S I P F C F L S V T A L L G 2 8687 42 A L L G N S L I L F AT I T Q 2 8688 44 L G N S L I L F A T I T Q P S 2 8689 49 I L F A T I TQ P S L H E P M 2 8690 52 A T I T Q P S L H E P M Y Y F 2 8691 57 P S LH E P M Y Y F L S M L S 2 8692 58 S L H E P M Y Y F L S M L S A 2 869361 E P M Y Y F L S M L S A T D L 2 8694 62 P M Y Y F L S M L S A T D L G2 8695 4 S T L Q N I T S T S I I F L L 1 8696 9 I T S T S I I F L L T GV P G 1 8697 19 T G V P G L E A F H T W I S I 1 8698 HLA-DRB1*0401(DR4Dw4) 15 - mers, v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5score SEQ ID 48 L I L F A T I T Q P S L H E P 28 8699 3 T S T L Q N I TS T S I I F L 26 8700 21 V P G L E A F H T W I S I P F 26 8701 45 G N SL I L F A T I T Q P S L 26 8702 60 H E P M Y Y F L S M L S A T D 26 870327 F H T W I S I P F C F L S V T 22 8704 32 S I P F C F L S V T A L L GN 22 8705 61 E P M Y Y F L S M L S A T D L 22 8706 11 S T S I I F L L TG V P G L E 20 8707 15 I F L L T G V P G L E A F H T 20 8708 18 L T G VP G L E A F H T W I S 20 8709 37 F L S V T A L L G N S L I L F 20 871047 S L I L F A T I T Q P S L H E 20 8711 20 G V P G L E A F H T W I S IP 18 8712 31 I S I P F C F L S V T A L L G 18 8713 38 L S V T A L L G NS L I L F A 18 8714 13 S I I F L L T G V P G L E A F 16 8715 24 L E A FH T W I S I P F C F L 16 8716 34 P F C F L S V T A L L G N S L 16 871762 P M Y Y F L S M L S A T D L G 16 8718 6 L Q N I T S T S I I F L L T G14 8719 12 T S I I F L L T G V P G L E A 14 8720 28 H T W I S I P F C FL S V T A 14 8721 30 W I S I P F C F L S V T A L L 14 8722 35 F C F L SV T A L L G N S L I 14 8723 41 T A L L G N S L I L F A T I T 14 8724 46N S L I L F A T I T Q P S L H 14 8725 56 Q P S L H E P M Y Y F L S M L14 8726 2 I T S T L Q N I T S T S I I F 12 8727 4 S T L Q N I T S T S II F L L 12 8728 8 N I T S T S I I F L L T G V P 12 8729 10 T S T S I I FL L T G V P G L 12 8730 29 T W I S I P F C F L S V T A L 12 8731 33 I PF C F L S V T A L L G N S 12 8732 36 C F L S V T A L L G N S L I L 128733 39 S V T A L L G N S L I L F A T 12 8734 42 A L L G N S L I L F A TI T Q 12 8735 43 L L G N S L I L F A T I T Q P 12 8736 44 L G N S L I LF A T I T Q P S 12 8737 52 A T I T Q P S L H E P M Y Y F 12 8738 14 I IF L L T G V P G L E A F H 8 8739 40 V T A L L G N S L I L F A T I 8 874051 F A T I T Q P S L H E P M Y Y 8 8741 1 F I T S T L Q N I T S T S I I6 8742 5 T L Q N I T S T S I I F L L T 6 8743 7 Q N I T S T S I I F L LT G V 6 8744 9 I T S T S I I F L L T G V P G 6 8745 19 T G V P G L E A FH T W I S I 6 8746 22 P G L E A F H T W I S I P F C 6 8747 25 E A F H TW I S I P F C F L S 6 8748 50 L F A T I T Q P S L H E P M Y 6 8749 53 TI T Q P S L H E P M Y Y F L 6 8750 55 T Q P S L H E P M Y Y F L S M 68751 57 P S L H E P M Y Y F L S M L S 6 8752 58 S L H E P M Y Y F L S ML S A 6 8753 59 L H E P M Y Y F L S M L S A T 6 8754 HLA-DRB1*1101 15 -mers, v.1B: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score SEQ ID 34 PF C F L S V T A L L G N S L 23 8755 61 E P M Y Y F L S M L S A T D L 228756 15 I F L L T G V P G L E A F H T 20 8757 11 S T S I I F L L T G V PG L E 19 8758 12 T S I I F L L T G V P G L E A 19 8759 27 F H T W I S IP F C F L S V T 16 8760 32 S I P F C F L S V T A L L G N 16 8761 48 L IL F A T I T Q P S L H E P 16 8762 37 F L S V T A L L G N S L I L F 148763 51 F A T I T Q P S L H E P M Y Y 14 8764 21 V P G L E A F H T W I SI P F 13 8765 28 H T W I S I P F C F L S V T A 13 8766 47 S L I L F A TI T Q P S L H E 13 8767 57 P S L H E P M Y Y F L S M L S 13 8768 60 H EP M Y Y F L S M L S A T D 13 8769 3 T S T L Q N I T S T S I I F L 128770 9 I T S T S I I F L L T G V P G 12 8771 18 L T G V P G L E A F H TW I S 12 8772 41 T A L L G N S L I L F A T I T 12 8773 46 N S L I L F AT I T Q P S L H 12 8774 62 P M Y Y F L S M L S A T D L G 11 8775 13 S II F L L T G V P G L E A F 10 8776 24 L E A F H T W I S I P F C F L 108777 8 N I T S T S I I F L L T G V P 9 8778 14 I I F L L T G V P G L E AF H 9 8779 6 L Q N I T S T S I I F L L T G 8 8780 20 G V P G L E A F H TW I S I P 8 8781 23 G L E A F H T W I S I P F C F 8 8782 25 E A F H T WI S I P F C F L S 8 8783 52 A T I T Q P S L H E P M Y Y F 8 8784 30 W IS I P F C F L S V T A L L 7 8785 31 I S I P F C F L S V T A L L G 7 878635 F C F L S V T A L L G N S L I 7 8787 38 L S V T A L L G N S L I L F A7 8788 40 V T A L L G N S L I L F A T I 7 8789 44 L G N S L I L F A T IT Q P S 7 8790 2 I T S T L Q N I T S T S I I F 6 8791 36 C F L S V T A LL G N S L I L 6 8792 42 A L L G N S L I L F A T I T Q 6 8793 43 L L G NS L I L F A T I T Q P 6 8794 45 G N S L I L F A T I T Q P S L 6 8795 53T I T Q P S L H E P M Y Y F L 6 8796 56 Q P S L H E P M Y Y F L S M L 68797 33 I P F C F L S V T A L L G N S 4 8798 49 I L F A T I T Q P S L HE P M 3 8799 1 F I T S T L Q N I T S T S I I 2 8800 4 S T L Q N I T S TS I I F L L 1 8801 5 T L Q N I T S T S I I F L L T 1 8802 7 Q N I T S TS I I F L L T G V 1 8803 16 F L L T G V P G L E A F H T W 8804 part 3HLA-DRB1*0101 15 - mers, v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5score SEQ ID 7 M I A N T Y L L T S P L M N P 23 8805 8 I A N T Y L L T SP L M N P V 23 8806 1 P A Y V H T M I A N T Y L L T 22 8807 2 A Y V H TM I A N T Y L L T S 17 8808 3 Y V H T M I A N T Y L L T S P 17 8809 9 AN T Y L L T S P L M N P V I 17 8810 11 T Y L L T S P L M N P V I Y S 178811 5 H T M I A N T Y L L T S P L M 16 8812 10 N T Y L L T S P L M N PV I Y 16 8813 12 Y L L T S P L M N P V I Y S V 16 8814 15 T S P L M N PV I Y S V K T K 16 8815 13 L L T S P L M N P V I Y S V K 13 8816 6 T M IA N T Y L L T S P L M N 10 8817 14 L T S P L M N P V I Y S V K T 9 88184 V H T M I A N T Y L L T S P L 8 8819 HLA-DRB1*0301 (DR17) 15 - mers,v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score SEQ ID 1 P A Y V HT M I A N T Y L L T 19 8820 2 A Y V H T M I A N T Y L L T S 16 8821 10 NT Y L L T S P L M N P V I Y 14 8822 11 T Y L L T S P L M N P V I Y S 148823 4 V H T M I A N T Y L L T S P L 13 8824 5 H T M I A N T Y L L T S PL M 11 8825 7 M I A N T Y L L T S P L M N P 10 8826 13 L L T S P L M N PV I Y S V K 10 8827 15 T S P L M N P V I Y S V K T K 10 8828 3 Y V H T MI A N T Y L L T S P 9 8829 12 Y L L T S P L M N P V I Y S V 7 8830 9 A NT Y L L T S P L M N P V I 5 8831 14 L T S P L M N P V I Y S V K T 4 88328 I A N T Y L L T S P L M N P V 2 8833 6 T M I A N T Y L L T S P L M N 18834 HLA-DRB1*0401 (DR4Dw4) 15 - mers, v.2: 238P1B2 Pos 1 2 3 4 5 6 7 89 0 1 2 3 4 5 score SEQ ID 2 A Y V H T M I A N T Y L L T S 18 8835 3 Y VH T M I A N T Y L L T S P 18 8836 7 M I A N T Y L L T S P L M N P 188837 8 I A N T Y L L T S P L M N P V 18 8838 12 Y L L T S P L M N P V IY S V 18 8839 9 A N T Y L L T S P L M N P V I 16 8840 4 V H T M I A N TY L L T S P L 14 8841 5 H T M I A N T Y L L T S P L M 14 8842 11 T Y L LT S P L M N P V I Y S 14 8843 15 T S P L M N P V I Y S V K T K 14 8844 1P A Y V H T M I A N T Y L L T 8 8845 10 N T Y L L T S P L M N P V I Y 88846 14 L T S P L M N P V I Y S V K T 6 8847 HLA-DRB1*1101 15 - mers,v.2: 238P1B2 Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 score SEQ ID 1 P A Y V HT M I A N T Y L L T 12 8848 5 H T M I A N T Y L L T S P L M 12 8849 10 NT Y L L T S P L M N P V I Y 12 8850 9 A N T Y L L T S P L M N P V I 108851 2 A Y V H T M I A N T Y L L T S 8 8852 7 M I A N T Y L L T S P L MN P 8 8853 11 T Y L L T S P L M N P V I Y S 8 8854 15 T S P L M N P V IY S V K T K 8 8855 4 V H T M I A N T Y L L T S P L 7 8856 8 I A N T Y LL T S P L M N P V 7 8857 12 Y L L T S P L M N P V I Y S V 7 8858 13 L LT S P L M N P V I Y S V K 7 8859 6 T M I A N T Y L L T S P L M N 6 886014 L T S P L M N P V I Y S V K T 8861

TABLE XX Frequently Occurring Motifs avrg. % Name identity DescriptionPotential Function zf-C2H2 34% Zinc finger, C2H2 type Nucleicacid-binding protein functions as transcription factor, nuclear locationprobable cytochrome b N 68% Cytochrome b(N- membrane bound oxidase,generate superoxide terminal)/b6/petB ig 19% Immunoglobulin domaindomains are one hundred amino acids long and include a conservedintradomain disulfide bond. WD40 18% WD domain, G-beta repeat tandemrepeats of about 40 residues, each containing a Trp-Asp motif. Functionin signal transduction and protein interaction PDZ 23% PDZ domain mayfunction in targeting signaling molecules to sub-membranous sites LRR28% Leucine Rich Repeat short sequence motifs involved inprotein-protein interactions pkinase 23% Protein kinase domain conservedcatalytic core common to both serine/threonine and tyrosine proteinkinases containing an ATP binding site and a catalytic site PH 16% PHdomain pleckstrin homology involved in intracellular signaling or asconstituents of the cytoskeleton EGF 34% EGF-like domain 30-40amino-acid long found in the extracellular domain of membrane-boundproteins or in secreted proteins rvt 49% Reverse transcriptase(RNA-dependent DNA polymerase) ank 25% Ank repeat Cytoplasmic protein,associates integral membrane proteins to the cytoskeleton oxidored q132% NADH- membrane associated. Involved in protonUbiquinone/plastoquinone translocation across the membrane (complex I),various chains efhand 24% EF hand calcium-binding domain, consists ofa12 residue loop flanked on both sides by a 12 residue alpha- helicaldomain rvp 79% Retroviral aspartyl protease Aspartyl or acid proteases,centered on a catalytic aspartyl residue Collagen 42% Collagen triplehelix repeat extracellular structural proteins involved in (20 copies)formation of connective tissue. The sequence consists of the G-X-Y andthe polypeptide chains forms a triple helix. fn3 20% Fibronectin typeIII domain Located in the extracellular ligand-binding region ofreceptors and is about 200 amino acid residues long with two pairs ofcysteines involved in disulfide bonds 7tm 1 19% 7 transmembrane receptorseven hydrophobic transmembrane regions, with (rhodopsin family) theN-terminus located extracellularly while the C-terminus is cytoplasmic.Signal through G proteins

TABLE XXI Motifs and Post-translational Modifications of 238P1B2 cAMP-and cGMP-dependent protein kinase phosphorylation site. 176-179 RKeT(SEQ ID: 8862) Protein kinase C phosphorylation site. 235-237 SvK Caseinkinase II phosphorylation site.  9-12 SatD (SEQ ID: 8863) 50-53 TvmE(SEQ ID: 8864) 130-133 SctD (SEQ ID: 8865) 172-175 SpeE (SEQ ID: 8866)N-myristoylation site. 14-19 GLsiST (SEQ ID: 8867) G-protein coupledreceptors family 1 signature. 52-68 MESsvLlaMAFDRFvaV (SEQ ID: 8868)G-protein coupled receptors family 1.  1-234

TABLE XXII Physical Features of 238P1B2 Bioinformatic Program Outcome238P1B2 Variant 1A ORF ORF finder 3758 bp Protein length 254 aaTransmembrane TM Pred N terminus intracellular, 6 TM region TM helicesat 3-29, 44-62, 86-110, 144-161, 182-203, 217-236aa HMMTop N terminusintracellular, 6TM TM helices at 6-28, 43-62, 86-105, 136-158, 180-203,216-235aa Sosui Membrane protein, 6TM TM helices at 6-28, 42-64, 87-109,144-166, 187-209, 217-237aa TMHMM N terminus intracellular, 6TM TMhelices at 7-29, 44-66, 86-108, 142-164, 185-207, 212-234aa SignalPeptide Signal P cleavage site between 169-170aa pI pI/MW tool pI 9.24Molecular weight pI/MW tool 28.59 kDa Localization PSORT 60% plasmamembrane, 42.9% mitochondrial inner membrane, 40% Golgi, 30% endoplasmicreticulum membrane PSORT II 44.4% endoplasmic reticulum, 22.2% plasmamembrane Motifs Pfam 7TM receptor (rhodopsin family) Prints Olfactoryreceptor signature, Type III secretion system inner membrane R protein,fibronectin Type III repeat signature Blocks no significant motif238P1B2 Variant 1B ORF ORF finder 3758 bp Protein length 316 aaTransmembrane TM Pred N terminus extracellular, 8 TM region TM helicesat 9-27, 33-51, 75-91, 98-125, 145-171, 206-226, 249-265, 276-296aaHMMTop N terminus extracellular, 7TM TM helices at 29-53, 66-90,105-124, 148-171, 202-226, 241-265, 278-297aa Sosui Membrane protein,8TM TM helices at 2-24, 33-55, 67-89, 104-126, 149-171, 206-228,245-267, 279-299aa TMHMM N terminus intracellular, 7TM TM helices at30-52, 65-87, 102-124, 145-167, 204-226, 247-269, 274-296aa SignalPeptide Signal P cleavage site between aa 26 and 27 pI pI/MW tool pI9.03 Molecular weight pI/MW tool 35.34 kDa Localization PSORT 64% plasmamembrane, 46% Golgi, 37% endoplasmic reticulum membrane PSORT II 44.4%endoplasmic reticulum, 33.3% plasma membrane Motifs Pfam 7TM receptor(rhodopsin family), polysaccharide biosynthesis protein Prints Olfactoryreceptor signature, Type III secretion system inner membrane R protein,fibronectin Type III repeat signature Blocks no significant motif

TABLE XXIII Exon compositions of 238P1B2 v.1 Exon Number Start End Exon1 1 3758

1. An isolated 238P1B2 protein comprising the amino acid sequence of SEQID NO.
 8873. 2. The 238P1B2 protein of claim 1, further comprising aheterologous polypeptide.
 3. The 238P1B2 protein of claim 2, wherein theheterologous polypeptide is an antigen.
 4. An isolated antibody orfragment thereof that specifically binds to a 238P1B2 polypeptidecomprising the amino acid sequence of SEQ ID NO:
 8873. 5. The antibodyor fragment thereof of claim 4, which is monoclonal.
 6. A recombinantprotein comprising the antigen binding region of a monoclonal antibodyof claim
 5. 7. The antibody or fragment thereof of claim 4, which islabeled with an agent.
 8. The antibody or fragment thereof of claim 7,wherein the agent is selected from the group consisting of aradioisotope, fluorescent compound, bioluminescent compound,chemiluminescent compound, metal chelator, and enzyme.
 9. The antibodyor fragment thereof of claim 7, wherein the agent is a cytotoxic or atherapeutic agent.
 10. The antibody or fragment thereof of claim 9,wherein the cytotoxic agent is selected from the group consisting ofricin, ricin A-chain, doxorubicin, daunorubicin, taxol, ethidiumbromide, mitomycin, etoposide, teniposide, vincristine, vinblastine,colchicine, dihydroxy anthracenedione, actinomycin, diphtheria toxin,Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin Achain, alpha-sarcin, gelonin, mitogellin, phenomycin, enomycin, curicin,calicheamicin, saponaria officinalis inhibitor, and glucocorticoid. 11.The antibody or fragment thereof of claim 9, wherein the radioisotope isselected from the group consisting of ²¹²Bi, ¹³¹I, ⁹⁰Y, and ¹⁸⁶Re.
 12. Ahybridoma producing a monoclonal antibody of claim
 5. 13. A single chainantibody that comprises the variable domains of the heavy and lightchains of a monoclonal antibody of claim
 5. 14. A pharmaceuticalcomposition that comprises the antibody or fragment of claim 4 and apharmaceutically acceptable carrier.
 15. A method of delivering acytotoxic or therapeutic agent to a cell that expresses a 238P1B2protein comprising the amino acid sequence of SEQ ID NO. 8873,comprising: providing a cytotoxic agent or therapeutic agent conjugatedto the antibody or fragment of claim 4; and exposing the cell saidconjugate.
 16. The method of claim 15, wherein the cytotoxic agent orthe therapuetic agent is selected from the group consisting of aradioisotope, fluorescent compound, bioluminescent compound,chemiluminescent compound, metal chelator, and enzyme.
 17. The method ofclaim 16, wherein the cytotoxic agent is selected from the groupconsisting of ricin, ricin A-chain, doxorubicin, daunorubicin, taxol,ethidium bromide, mitomycin, etoposide, teniposide, vincristine,vinblastine, colchicine, dihydroxy anthracenedione, actinomycin,diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin Achain, modeccin A chain, alpha-sarcin, gelonin, mitogellin, phenomycin,enomycin, curicin, calicheamicin, saponaria officinalis inhibitor, andglucocorticoid.
 18. The method of claim 15, wherein the radioisotope isselected from the group consisting of ²¹²Bi, ¹³¹I, ⁹⁰Y, and ¹⁸⁶Re.
 19. Amethod for detecting a 238P1B2 protein comprising the amino acidsequence of SEQ ID NO. 8873 in a biological sample, comprising:contacting the biological sample and a control sample with the antibodyof fragment thereof of claim 4 that specifically binds to the 238P1B2protein; and determining the amount of 238P1B2 protein and antibody orfragment thereof complex present in the biological sample and thecontrol sample.
 20. The method of claim 19, wherein the presence of238P1B2 protein in the biological sample relative to the control sampleprovides an indication of the presence of cancer.
 21. The method ofclaim 20, wherein the cancer is prostate cancer.